Is it permissible to offer the make-up of six days of missed prayers before making up 40 or 41 days of prayers that were missed previously?

It is not permissible to abandon prayer as long as one is of sound mind, and there is no excuse that waives it except the removal of accountability. The basic principle for making up missed prayers is to do so in order, starting with the earliest then the one after it. However, jurists differ on the obligation of observing this order among missed prayers. What you did, prioritizing the make-up of the six-day prayers over the forty-day prayers, absolves your responsibility according to many scholars. The Shafi'is consider the order to be recommended, not obligatory, while the Malikis consider it obligatory with remembrance, but it is not a conditional obligation, so if the order is violated, the prayers are not invalidated. We advise maintaining prayer at its prescribed time, and if it is missed, then it should be made up in order.