Let me ask you this questions, you get HQ ilv70 gear made and meld it to be the best it can be currently for you. You get some other ilv90 part, and this changes something so you should change 2 materia to be best you can be. If you want to make this change why cant you just drop 2 materia (any 2, 1 at a time) and remeld the extra 2 and be done. You shouldnt need to clear all 5 and start over. This is all the OP is really saying, he just used a derp moment an an example of one way you might want to remeld.

My old Coil BLM had to change a few melds for acc after getting his coil body to meet cap, just 2 changes and had to clean all and start over which was really not needed as 3/5 were kept the same.