One of my users found out if you rename a file in a synced folder that is set for "sync both ways", it deletes both the file that was renamed on the share and the file in DMX on the next sync.

There are limitations to the sync both ways, yes. What happens is the following:
- let's say the user adds file a remotely
- when the sync process runs it finds the file a that has recently been created and does not exist in DMX so it imports it
- the user renames a to b
- the process returns and sees an old file called b. It assumes that b has been deleted in DMX in the meantime and deletes b from the source
So the crux is in the timing. DMX does its best to determine the file modification date. But Windows doesn't make this very easy to say the least. So in the case of renaming there is actually no difference between the old and new except the name. The time stamp remains the same.

Note if you have "Source Leading" you don't have this issue, but it is of course a different sync strategy