Gotcha. If your client is on the Ultimate Linux plan, I don't think you'll be able to get to the migration tool, unfortunately. (That's just for the Managed WP plans.) In that case, you should be able to spool all the plugins back up; they're only restricted on the MWP side of things.
One option is to ask your client to cancel the Ultimate plan, and instead get the MWP plan, if that's a better fit.
Net: You should be fine either way, but lemme know if I can help.
P.S. The other-other option is if you've already done a bunch of work on the Ultimate plan side w/ setup, I can see if it's possible to bounce your client's account from the Ultimate Linux plan (which is unmanaged) to the MWP side of things, which would take a lot of the burden off you down the road. (It handles caching and backups and has staging sites and all that good stuff.)