My understanding here is that you have a top-level model that is protected. Within this protected model, you have several model references. When you made those models protected as well, you ran into issues when you loaded the top-level model again.
According to MATLAB R2020a documentation, the root cause is that a model you protect cannot reference a protected model directly or indirectly. When you first protect the top-level model, none of the model references are protected, which is why you were able to do so. However, after you protected the models referenced by the top-level model, the top-level model is now referencing protected models, which is not allowed in R2020a. As a result, when you load the top-level model again, it is complaining about the lower level model reference having been modified.
As workaround, you may convert the model reference blocks in your top-level model to their equivalent atomic subsystems. Doing so would ensure that not only will you be able to properly protect your top-level model, but also you will be able to properly protect the modules within your model as well. Most importantly, it will resolve the error you are seeing when you load the top-level model.
Best Answer