After removing the mylar i noticed that most of the inserts were loose

They have cupping and will have to flatten them .

I am unsure on how to do this ?

Remove the cupped insert. Be careful if there is art on the insert, as this may cause an issue. Use a block of wood roughly the size of a sanding block, and cut the desired wet sandpaper to fit and overlap the wood. place in the vice. Spray water or windex on the sandpaper. Face down, start to sand the insert, going in circles. Observe the insert. If it has artwork starting to sand off - STOP. If not, keep going. continually check that the insert is starting to level. Change to a higher grit. Start at 400, 600, 800 (to flatten) then 1000, 1500 and finally 2000. Polish with novus 2.

Repeat for all the inserts.

If art is being sanded off - Plan B - Find an insert decal kit.

The other option is to buy all new inserts and decals.