hi,
I believe FlashMagic functionally is equivalent to FLIP? in the Atmel world.

I never tried FlashMagic so cannot say either yes or no. FLIP is just Win$lows/Linux program which downloads program/data into Atmel`s chips via ISP/bootloader based on RS-232/USB/CAN. It has options for loading hex-file, read/erase/write device, edition of binary file (inside buffer area editor) and setting configuration/protect bytes and bits.
Oh, it supports ISP via bootloader only (i.e. "intelligent" one using software which executes built-in bootloader API functions); it does not support ISP via SPI interfaces (so no AT89S51/52/53/8252 chips are supported - these chips has both parallel/SPI hardware programming).

Finally, I doubt that the problem is in FLIP; you know, it is Atmel and could you even imagine that during rename T89C51RD2 to AT89C51RD2 they eject from the chip 2kb of EEPROM and insert alot of "features" which are not compatible with previous revision of the chip.

The simplest way I see which may help original poster is just load source code into Keil and RECOMPILE it again for new device. Indeed it shows some/many errors which must be fixed manually... But it is only one correct may when you migrate from Atmel to Atmel production. Unfortunately it seems that original poster has not Keil or source files. Allas.

Regards,
Oleg