Hi,
AFAIK RAppID bootloader performs mass erase of code flash before programming.
If you intend to keep some data between two programming sessions you can
1) save the address range before programming into s-record
2) merge the s-record with your firmware s-record
3) erase & program merged s-record file
Alternatively you can program your data into an alternative memory (DFLASH, UFASH) by JTAG probe. These memories are not erased by RappID Bootloader.
Hope it helps.
Stan