Before I run some tests I was wondering if anyone knows offhand if most UxROM games actively write to CHR-RAM after loading at power on and copying the data from PRG-ROM to CHR-RAM? Or is it just the one time thing and then never written to again?
This would be pretty easy to check in emulator like Nintendulator. The answer is that yes, most games actively rewrite CHR-RAM depending what they need. If you think about it their tileset would be VERY restricted otherwise (512 tiles is not a lot).
E: Games like Battletoads (although it's AxROM) even animate the characters by updating CHR-RAM.
Yeah, most CHR-RAM games update CHR-RAM quite frequently. They do it at least between levels and such, but usually more often than that.
Open some games in FCEUX and open the PPU viewer. There you can see the current state of the pattern tables, and it's usually easy to see when tiles are being rewritten.
Megaman 6 writes enemy tiles on the fly before they appear on the screen.