newRPL - build 1255 released! [updated to 1299]

[3298]

Okay, so the offset means your 39gs probably had a different (newer?) version of the bootcode, but at least not a totally different one (kind of expected, to be honest). Of course I can't tell if the differences included something for the slightly different hardware configuration, but I think you could try just taking the 50g bootcode from x49gp and writing that onto the flash. I mean, what can go wrong that makes the situation worse than it is now?
Since the necessary part of the boot sector miraculously survived, you could even preserve the device's serial number (the last few bytes of the boot sector) by copying it over into the replacement boot sector. You'll recognize it, in x49gp it's the ASCII string "DEA0000001" for the 50g bootcode or "DE00000001" for the 49g+ one.

About writing to the flash, did you follow the normal flash-writing procedure consisting of a sequence of specific bytes written to specific offsets? If not, check out flash.c from the x49gp sources for details, specifically the function flash_put_halfword.