Plastic deformation, buttons not removed for trays to be used without buttons

My doctor failed to remove my buttons on the last two sets which were made for use without buttons. I had lots of pain and changes in my bit as a consequence - apparently my teeth got pushed up during this process. The Doctor removed the buttons and wants me to wear the last set for 6 weeks to let the teeth settle back and come back down.  I am wondering if that set should be replaced so it is true.  Wondering how wearing the liners with buttons where there is no accommodation for such might impact the plastic or if the plastic is strong enough to withstand 336+ hours of wear with interference and no deformation.