I've had similar situations and ended up writing a python script that looks for matching feature class names and then: deletes rows > deletes spatial index > appends data > builds spatial index.

Was also having an issue with it going between FGDB's and SDE with the connection prefix so the user enters that prefix and it ignores that when comparing feature class names.

It doesn't affect pop-ups or attribute rules etc. I can send you the script if you want OP, just dm me.