Update causes objects I didnt change to modified status

Hi All,   We are noticing a strange issue in our env where when we perform an update in MX Studio Pro 9 against our git repo, all the sudden objects we didn’t touch show up in our local project as modified.  The only way to fix this is to delete the project and pull from the repo again but this can cause any un-pushed work to be lost.  Any suggestions on what could be happening here?   Thanks
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