If I use the IDE to rename the fields mapped on relations for all my entities, and then use the IDE refresh the schema, will the names be reset back to the original or will they remain intact.

Surely they remain intact, but I just renamed the fields on about 100 entities and I dont want to find out the hard way.

They should stay the same, as the name is migrated from the old relation to the new relation. (you always have the backup if something goes wrong. IF something goes wrong (but I haven't seen it go wrong) please let me know.