Stripping and saving brings up the usual popups about are you sure you want to save, etc. The problem was trying to select a mech to re-equip it. Selecting any of the invalid wave 3 mechs, the "save" button was greyed out.
For a few minutes I was a little panicked about being unable to access any of my Jaguar and Koala variants. Knowing a thing or two about QA (from friends who worked at Bioware) I exited the client, tried to reproduce the issue again. Same issue, couldn't select any of the mechs when starting from the home screen.
I then tried to access the select mech screen from somewhere other than the home tab. Go into Skills, click around the new chassis, then go to select mech. Voila. You can properly select and equip an invalid mech.
Try to access another one from the home screen, no luck. Try again through the Skills tab first, and it works.
Note: I have a few stripped IS mechs that I can select without issue from the home screen. No need for the workaround.
Edited by Luscious Dan, 17 June 2015 - 12:01 PM.