nrf5340 2.6 to 2.9 migration issues

We have developed device that used 2.6 and when moving to 2.9 everything broke apart and I cant get it to boot and I cant get any output from device. Be it from USB or SWD pins (as its custom board). 

It worked a week ago but one day it just broke, note that it worked for months on 2.9. I've isolated the issue to configuration and not code. 

As I need P0.11 and P0.09 I've remaped them based on 

 RE: nrf5340 Gpio forwarder availibility 

but that triggered something in build. It looked like there were some remnant 2.6 configs or something. 

Now, im totaly confused. Anything I do results in failed compilation and if it does not for some reason or a another (a lot of testing) the device wont boot and I cant get any debug information out of it. 

Please provide what files or info you need to help me diagnose this issue.

Regards, 

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