It might be caused by the same issue as in this thread. The engine is re-copying the InsertPacks every startup.
UE 5.4 editor startup keeps re-copying StarterContent
Removing the InsertPack line for the StarterContent from the DefaultGame.ini is a workaround.
InsertPack=(PackSource="StarterContent.upack,PackName="StarterContent")
Is the re-copy at every launch by design or is that an issue?
Is it possible to check with the Revision Control System first if a file/directory is ignored before adding it to avoid the slow file-by-file add operations?