MATLAB: Overwriting information in a cell array

cellcell arraysfunctionshandlesindexindexingMATLABmatricesmatrix manipulationvariables
I am working with cell arrays and matrices. I am trying to overwite information in a cell but instead it places the new data into a new cell and retains a copy of the old data in a deeper cell if that makes sense. As a result, when I try to index into the cells I am grabbing the old data instead of the information I am looking for. I read the cell array page and thought I understood, but I guess I am missing something. The cell array in question is BranchMatrixRevised. If someone could help me either index into the proper cell or overwrite the old information that would be great. My code is below.
clear
close
clc
A = [0,0,0;0.00977495601952172,0.0129188554738323,0.999868768093125;-0.566794094824837,-0.823750570492204,0.0133959578031223;0.0279587435128966,0.0380588867245362,1.99938731654588;0.830388266617646,0.583999369869120,0.978401571089338;-1.07826433834531,-1.64452537544960,0.267810795303313;0.168715496407312,0.263085998125572,2.96351922435162;-0.791458202545459,0.611268411797120,0.998070417818667;-1.41124221175034,-0.289407593850698,0.0506110237693017;1.69942938355116,1.04462646221878,1.15892918358242;-1.55216375501531,-2.44987966243271,0.623934110066297;0.188310075544404,0.501770043093754,3.93441879647330;-1.44603145623221,1.35107113546187,1.15371676572365;-2.35391403973316,0.0183196401577155,0.179737992978120;2.59879677816763,1.38804628951095,1.42948622326796;-1.92629974765512,-3.28302931738291,1.03122259685150;0.190461468181228,0.731318108759712,4.90771374511875;-2.01837467713375,2.14014570650778,1.37684130228734;-3.30531517848174,0.217844651708771,0.414313445558867;3.50709118523837,1.65551615551852,1.75113998255253;-2.23204460424917,-4.13488361866807,1.45650407075820;0.193343935566412,0.934427321909631,5.88686559182864;-2.51244231909718,2.97180232130260,1.63030617210704;-4.25650570961388,0.357419056329789,0.689550723301627;4.41845060685608,1.87363023778730,2.10021053665969;-2.47842156351806,-4.99324597672323,1.90651791078471;0.204283419234320,1.13357858075284,6.86677329350173;0.617793464714887,0.0559247730198438,6.10612769252045;-2.96417360323821,3.81704174520463,1.91580426879081;-5.20242439373799,0.476408999682868,0.991344090368801;5.32672360772571,2.06445068867013,2.47253796167180;-2.69346338350278,-5.85030685131976,2.37470982965291;0.218591936197924,1.32878562119851,7.84743096960627;-3.26247612265381,-4.91985596911837,1.29018005288354;1.20197539596291,-0.580347098756520,6.61000225666269;-3.37592827171665,4.67443410026770,2.22457026832058;-6.14584567995603,0.584770610127789,1.30473528056482;6.23299868743130,2.22581272192086,2.86321400922248;-2.89467385558292,-6.70726873056154,2.84918921113506;0.209717491582492,1.53184472980862,8.82655723451965;5.28440710514136,1.17097130314088,2.91964410258613;0.576278852478300,2.24513662818586,7.66753960818188;-4.04653068178957,-4.84646596151352,0.673842194982372;1.72465217643194,-1.18852390077965,7.20743841278270;-3.76500316313530,5.53715317053961,2.54758193166533;-7.08499357301506,0.666849489054822,1.63829830698843;7.13773556686645,2.38268963160310,3.25924533904186;-3.08850223839479,-7.56458389242937,3.32609724340970;0.176682672356017,1.77636612069925,9.79563823738556;5.70892694024996,0.283366758099107,3.09836478191717;0.834848920291403,3.20098548783449,7.80716223363894;2.23645813228566,-1.80307906039568,7.80775218019269;-4.13663420978661,6.40608142770811,2.87446730769027;-8.01389420090031,0.739303774953617,2.00147044244114;8.04005085003118,2.54735749010561,3.65763161659614;-3.28567882346993,-8.41947317913047,3.80597816799600;0.151573909742903,2.03767830086445,10.7605659520551;-6.82918401328041,0.278600280775844,2.52363667248442;-3.41363523840503,-7.08870431609608,4.14330417016278;6.35396040499232,-0.474663609164808,3.19491420795479;1.06216210967955,4.10256481833496,8.17524296492560;2.75275937858220,-2.40442829800382,8.41751616527277;-4.49887555491066,7.27474744137621,3.21240304800297;-8.93747200633802,0.809847032829654,2.37833604988111;8.93679366464217,2.75035659507643,4.05087923302196;-3.49679202503365,-9.27121011623096,4.28553567873291;0.120474891403918,2.30220475044321,11.7244428158357;-6.57337445354577,-0.109648927503134,3.40897503798041;-3.90131441220521,-6.94494653825290,5.00440969491056;7.05097560070378,-1.18529470189817,3.29069138158143;1.32262284552297,4.97356081042056,8.59180771001900;3.28964279764057,-2.99261263184027,9.02232637002263;-4.85227421135047,8.14355948795292,3.55920993569369;-9.85594939518955,0.878289437178573,2.76784204913582;9.82550611659926,2.98592839011066,4.44419349302377;-3.72248319429006,-10.1171476702764,4.76870557719025;0.0788524583019931,2.54046289454804,12.6947523694476;2.70499218347696,-3.21391766868317,7.83232794441650;-2.84203085926377,-9.70887276953909,3.66930583711619;-6.31756489381112,-0.497898135782113,4.29431340347640;-4.51675110863053,-6.94038338635526,5.79258280428302;7.75826716048403,-1.87839080959415,3.42981878707837;1.60739083428736,5.83327554833172,9.01583337197052;3.81380630124427,-3.57090289370221,9.64749274349896;-5.21110077179350,9.00941019096056,3.90784450027642;-10.7701023523524,0.936847376158581,3.16895966118096;10.7111773842992,3.23085322898537,4.83865290649108;-3.95158917741763,-10.9629681728992,5.25047121091495;0.0248941422755761,2.76290060345524,13.6682049701363;-3.96468559986903,8.59207273742804,3.45422268973630;-4.53038653298116,-10.2195319906366,4.18835254129213;-0.734431529015096,3.08504028776024,12.4898020857790;-2.18726969349390,-10.1465354228472,3.05307599549947;-5.19378789303215,-7.06258274529947,6.51831588830272;8.48339326062922,-2.55215288868641,3.57207489297718;1.87742850700644,6.69346716517060,9.44844178339196;4.34166392226097,-4.13247115672692,10.2846798572246;-5.56586475306079,9.87609452074379,4.25855918503254;-11.6790955983398,1.00013474235130,3.58093780141378;11.5912722790929,3.48104407126623,5.24218421704439];
x = A(:, 1);
y = A(:, 2);
z = A(:, 3);
SizeofA = size(A,1);
dist1a = nan(numel(x)); % places nans on the diagonal after distance calculation
proximity = 1.000;
save_criteria = 3;
for i = 1:SizeofA  
    for j = 1:(i-1)
        dist1a(i,j) = sqrt((x(i)-x(j)).^2 + (y(i)-y(j)).^2 + (z(i)-z(j)).^2);
        dist1a(j,i) = dist1a(i,j);
    end
end
i2keep = find(sum((dist1a - proximity <= eps('single')), 2) >= save_criteria);
keep_x1 = x(i2keep);
keep_y1 = y(i2keep);
keep_z1 = z(i2keep);
B = [keep_x1, keep_y1, keep_z1];
C = 1:SizeofA;
index = ismember(C,i2keep);
D = A(~index,:);
%%








dist1b = pdist2(B, D);
[~, minRowIdx] = min(dist1b,[],1);
[GroupID, GroupList1] = findgroups(minRowIdx);
NeighborGroups1 = splitapply(@(x){x},D,GroupID(:));
SizeNG1 = size(NeighborGroups1,1);
%%
for i = 1:SizeNG1
    test1{i} = pdist2(B(GroupList1(i),:), NeighborGroups1{i});
end
%%
for i = 1:SizeNG1
    test4a = find(test1{1,i} - proximity <= eps('single'));
    test4b{i} = test4a;
end
%%
for i = 1:size(B,1)
    [BranchMatrix{i}]= BranchLinks(B(i,:));
end
%%
for i = 1:size(B,1)
    [NeighborMatrix] = NeighborDetector(test4b{i},NeighborGroups1{i});
    BranchMatrix{1,i} = [BranchMatrix(i), NeighborMatrix];
end
%%
x_c = 0;
y_c = 0;
z_c = 0;
Center = [x_c,y_c,z_c];
for i = 1:length(BranchMatrix)
    dist1c(i,:) = pdist2(Center,BranchMatrix{1,i}{1,1});
end
%%
BranchMatrixRevised = BranchMatrix;
for i = 1:length(BranchMatrixRevised)
    [DownstreamMatrix] = DownstreamDetector(Center,dist1c(i),BranchMatrix{1,i}{1,2});
    BranchMatrixRevised{1,i}= [BranchMatrixRevised(i), DownstreamMatrix];
end
%%
for i = 1:length(BranchMatrixRevised)
    dist1e{i,:} = pdist2(BranchMatrix{1,i}{1,2},D);
end
%%
function [NeighborMatrix] = NeighborDetector(test4b,NeighborGroups1)
for i = 1:length(test4b)
    NeighborMatrix(i,:) = NeighborGroups1(test4b(i),:);
end
end
function [BranchMatrix] = BranchLinks(B)
BranchMatrix = B;
end
function [DownstreamMatrix] = DownstreamDetector(Center,dist1c,BranchArray)
dist1d = pdist2(Center,BranchArray);
for i = 1:size(BranchArray,1)
    if  dist1c > dist1d(i) && length(dist1d) > 2 && dist1d(i) == min(dist1d)
        DownstreamMatrix(i,:) = NaN(1,3);
    else
        DownstreamMatrix(i,:) = BranchArray(i,:);
    end
end
end
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