It has nothing to do with Evenepoel, as they get along great and Evenepoel has repeatedly asked for Alaphilippe to be in his team. So if it were up to him, Alaphilippe would likely have done the Ardennes and not the cobbled classics. He again has asked for Alaphilippe to be on the TDF squad.
The team just felt the need to mix it up, as Alaph was simply not performing anymore for far too long. Maybe the program they gave him wasn't a success, but just to wait, do nothing and hope for things to magically change, was also not a solution. His results simply did not warrant him getting first choice in his program. If his results would still have been like they were 4 years ago, there is no doubt in my mind that he would still at the very least be co-leader in the Ardennes and would be going to the TDF.