To be certain of my comments, I need to see a few of the lines from the linker command file you are using. Just because it is easier, please attach the entire file to your next post.
[quote user="Stephen Phillips1"]is .text contiguously allocated or will the linker split it between FLASH and FLASH2[/quote]
Probably so. I need to see your link command file to be sure.
[quote user="Stephen Phillips1"]Also if the latter is the case (it floods into FLASH2) would it be a good or bad idea for the ISR functions to call another function if the code for the ISR gets a bit more than a few bytes (the biggest currently is 106 bytes and that makes me nervous as well).[/quote]
I'm sorry, but I just don't understand what you are asking here.
Thanks and regards,
-George