Yes that sounds like the efficient way to do it.It is much easier to rip the bandage off quickly. Much quicker and easier to do them in batches. Batch #1: your useful ships. Use up all your Data Mined Wake Exceptions. No problem, visit the mat traders, shuffle your mats down and on the next server tick do a bunch of missions that offer 20 G5 engineer mats per mission. Recover all your engineer mat bins. Then do another batch.
So instead I might try K Olley’s approach and make up some swap units for my least used ships.