No problem with mods when you put in a standalone unit. :E
I know what you mean though. When you tune a QR25 ECU with the SAFC, the ECU starts ignoring the inputs from the SAFC and eventually you go right back to the factory settings within a span of about 2 weeks. Nice, eh?
Is that because of OBDII or just the ecu?
Just the way they programmed the ECU to work. Silly Nissan! 
All the honda K series engines had the same issues actually. Its the addaptive ECU BS. Its kinda interesting on the new diesel trucks though… because they will program it with a power programmer just to show you what It could do, and then in a couple weeks when it kicks out you want to go buy it.
Thats the Bully Dog system isnt it?