Code U1421 after delete can I clear?

Just deleted my 2013 this past weekend and this morning the check engine light came on the code is u1421. I had the shop put EFI live and I did the the egr delete. Can I clear the code with my handheld Bosch scan tool or will it mess up the EFI live tune? I have read the code is just a impulse communication and can be cleared but i don't want to lock up my truck.

since when has clearing codes had any effect on a tune thats already flashed to the computer?

I wouldn't think it would have any effect but I was wanting to check since it was a code that is relating to the communication between the modules.