Before touching anything make sure the client PC Thunderbird profiles are backed up.
POP3 will only retrieve Inbox. Read online for why etc.
I think Thunderbird asks about IMAP/POP on setup. It's unlikely to change by itself. The automated account system setup possibly detected/guessed POP before IMAP. (Hence I use policies to stop this happening!)
Uninstalling - I think the data may be in the profile on the client unless you changed or deleted anything. But can't be sure. As you swapped versions there may be more than one profile in there.
https://support.mozilla.org/en-US/kb/profile-manager-create-and-remove-thunderbird-profilesCareful you do not start with an old POP profile - you may lose more mail!!
Use profile manager to see what Thunderbird sees. You can then look directly in the sub folders with a file browser. Make sure you can view hidden files & directories.
Unfortunately the reason I state in my sig to not ask about unsupported OS is I don't have W7 to test any more so can't help there. You are going to have dig in on the client PC and have a look.
You will likely need to use the latest version of Thunderbird as the profiles get modified on upgrade and old versions will have no access to them.
If you can then I'd try the following:
Remove the Thunderbird password database, or modify the server name, so when you restore the profile it does not collect more mail (or disable POP access on the server?)
If you can see the POP mail, create a new IMAP account to the right mail account.
Copy POP inbox to IMAP inbox
There may be other more manual methods that you can research.
Good luck.