Allow engine conversion to be registered

Servus together, I’m just having my car E46 Diesel remodeled at a company. A N54 (petrol) from the E90 series is being upgraded. The company had the promise of a Tüv examiner to enter the engine conversion before the conversion. Unfortunately, this examiner is no longer active. Now the company has informed me that it will be very difficult, if not impossible, to get this conversion registered and I am standing there now. The conversion now takes 1.5 years. Technically, everything is decent, brakes, suspension everything Official parts. They have offered me now instead of the N54 to install an M3 E46 engine, which I do not want, however, this conversion would not cause any problems with the registration according to their statements. I can not believe that it is such a problem to enter the conversion, because there are far more complex modifications. According to their statements I need a vehicle unspecific exhaust gas report of the engine. Now I do not know if they just want to push themselves before the more elaborate conversion, or if d he registration is really not possible. Would be really grateful if someone would speak out on this subject. MfG Manu