Simulink Three-Way Merge tool mixes library blocks

When using Simulink's three-way merge tool on a Simulink library the tool will automatically copy over missing or changed blocks from the branch being merged in. As in if I am merging branch2 into my local branch called branch1 the resulting merged model will contain library links to branch2's version of the block. This does not show as a problem while the merge tool is still open, the only indication being the library link icon in the lower left of the block. But when the tool is closed out and the model is attempted to be built it errors out and shows that its library block has a broken link ("branch2_model.slx not found"). Instead all these cases have to be found manually and the links broken. If a library block uses another library within it then there is no way to tell which branch it is coming from as it would have the link icon in the lower left either way.

Is there a way to prevent Simulink three way merge from doing this?

Thank you