There was a bug in recent versions with MUC if i recall correctly. So, updating to 4.2.1 would be useful probably. You can try disabling history for a particular room and then enable it again. Not sure if it will wipe all history from the database. You can also try destroying and recreating rooms to be sure that history is wiped.
Not sure what you meant about backup folders. You also haven’t mentioned what OS you are using. On Windows you can install 64-bit version on top of 32-bit. So when running the installer, you should manually point to C:\Program files (x86)\Openfire (if installed there) and it will uninstall 32-bit and install 64-bit version in that folder. You can then increase it more that just 2 GB, depends on memory amount on the server. You can just set it to 2000 or 3000, i don’t think it have to be in x2 increments (32, 64, 128, etc.).