I managed to complete this conversion project today and it turned out great...
The car had the factory file uploaded again and was stuck in limp mode after the first attempt failed and the files caused to the car to fail to start...
I got an XS evo cable with diagbox software for christmas...
My father in law came in this afternoon and I managed to recode the injectors and clear all faultcodes...
We testdrove the car and it was behaving like it was, prior to the first attempt again...
It was running rough and very smokey.

I uploaded the latest version of the remapped file and everything went as it should. Car started fine this time but was in limp mode again. Hooked diagbox up again to recode the injectors, only to find out that they were still coded and the check engine light and limp were gone...

As I wanted to go for a testdrive, the car was in limp again the next time we started it, turned it off, restarted and it was fine...

We did the testdrive and the car was flying through the gears without any smoke, so all was well...
We turned off the car and were happy with it...

As soon as my father in law wanted to head home, the car was in limp again and the check engine light on again...
Turned the car off again and restarted it and all was fine yet again... pretty weird?!?

Anyone got any clues on this?

ugh, wait... you uploaded a 110 HP file to 90 hp hardware?

110 hp has a VGT while 90 HP engine has a wastegate regulated turbocharger - N75 maps are totally different...

Did you check if there are any other differences in wiring or component types?

No, they accidently installed a 110BHP engine in a Citroen C4 1.6HDi90, so wiring, sensors, ecu and BSI are still factory (90BHP version)
But the entire engine was swapped, because the factory engine failed and it was cheaper to swap the engine.
I had nothing to do with this, I just offered to help...
The owner of the car sourced the engine himself and didn't know what to look for, to spot the differences...
Trust me, I know these engines inside and out ;)
ECU's I am pretty confident I know my stuff, but this is the first time I tried something like this...

I believe they kept the sensors that were mounted on the "new" engine, when they got it and reused the rest from the previous one, such as boost, intake temp, maf,... as well as the wiring loom...

I did not simply upload a 110 file, as I don't own a BDM, yet...
I mapped the 90 file to suit the different hardware, being the VGT and Injectors...
I changed the DW maps, TL's, NM to IQ's, boost maps, N75's, SOI's, Durations, Railmaps, and so on...

No DTCs recorded after a limp home mode? weird.. :eh:

Sometimes also requested MAF/EGR map does sutch problems. Also if requested and actual MAP don't fit.. Check vacuum hoses and vacuum valve for a turbo actuator too (EGR is electric on this engine)...

how did you convert the Turbo to VGT in the ecu?

I am installing a VGT turbo on a 90hp version but it is not controling correctly...

Thank you

Just to finish this topic off...
The issue was all coding got lost, not only injector codes but all of them.
Did a full manual recode and hasnt skipped a beat ever since.
It did however wreck a clutch and a gearbox ;)