You won't need frags in the future to make skillbooks

Well it's not like we'll get the tendo skillbreaks for a long while so don't worry about. Anyway, the skill break system uses items to modify the skills but unfortunately the system acts the same as purification so you have to protect certain skills you like before using the skill break system. Skill books still remain but you either have to craft them or buy them.

Like I said, fragments won't be needed. Once we get the update to the system, you'll be able to farm new items meant for crafting skillbooks in instances meant only for skillbook crafting. After that update, there is an another update, which is the system similar to the purification system I said in my previous reply. In respect to what to do with the fragments, you can either keep them in hopes of getting lucky with getting frags to 5* or refine them.