Eagle Change all part names (Designator)
There isn't a direct way to do this, but there is a ULP which is helpful in this regard called: swap.ulp

With this you can simply enter commands in eagle such as:

run swap R1 R10


That would swap the names of R1 and R10 (R1 becomes R10, and R10 becomes R1).

If you have lots to do, you can use a text editor to make a list of the swaps required to map all of the part names into the desired ordering. You can then convert your list into run swap a b commands and run all of them.