I think the admission committee won’t care.
They will use the LOR from your three professors to make a decision.
The LOR from your current supervisor might slightly be better, but it won’t change much if it is not there.
They won’t ask you about it, they will either accept you or decline you based on their own judgment from whatever’s available on their review day.
If you have publications from this project, that should tell enough about what you have done in these 3 years, i have never seen any research certificate whatsoever. I do not think the committee does either.