Apart from needing to replace the commas in your array by periods, I don't see where you went wrong. The RE seems fine and the way I read the documentation for regexprep this should work as you expected.
Since I can't fix your code, I wrote some new code that should do the same as what you intended:
substr={'B0.2Si0.05'};
numarray = [0.184320000000000 0.0460800000000000];
c=arrayfun(@(x) sprintf('%.5f',x), numarray, 'uni', false);
re='(\d+)(?:\.(\d{1,2}))?';
split=regexp(substr{1},re,'split');
txt=split(:)';
k=1:min(numel(c),numel(txt));
txt(2,k)=c(k);
txt(cellfun('isempty',txt))={''};
newSubstr=horzcat(txt{:});
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