This depends on what kind of file you're talking about. mat files and m files are very portable, especially if you leave the defaults as they are. R2020a changed the default encoding to UTF-8, but that doesn't matter if you don't use special characters like é.
Files for Simulink can be fairly tricky, and the mlapp format changed in R2018a. I don't know if that last one matters for you.
Bottom line: if you stick to mat files and to m files without special characters, everything will work from R2006b onward. I don't see big changes to this happening in the foreseeable future. (I don't work for Mathworks and have no inside information on future plans)
