Hi @pemitchell,
Version numbers are different for Pro and Free version, to make sure that you have pro installed version number should be 1.x and if you see 4.x that means free is installed.
If you disable both Membership 2 Pro and WPMU DEV Dashboard plugins then WordPress will check free version number and if you perform the update you will get the free version, but as long as any of these two plugins are active you shouldn’t see notification to update to 4.x
I’m guessing that this happened and that you “updated” to free version.
If you have any other questions about the Pro version please start a new chat on our site and we will gladly assist you further.
Cheers,
Predrag