How do I restore iCloud mailboxes from Time Machine without losing new mail?

Question

This morning when I opened my laptop and checked my email, Apple Mail decided to flag every single email in my three separate Apple-related accounts ([email protected],[email protected], and [email protected])—some 14,500+ emails total. None of the emails in my comcast or yahoo accounts were affected. Of course, each of the three accounts is set to download copies to my laptop as well as keep them on the server, so now all of those emails are flagged across the board—on my iMac, my iPhone, my iPad mini as well as my laptop. Yay. Since some of the emails were actually flagged intentionally by me over time, I don't want to just unflag everything or I'll lose my flags as well as the ones spontaneously generated this morning.
My questions are:
1) If I use a Time Machine backup from last night to restore the three affected mailboxes, will iCloud accept them as the de facto most up-to-date versions, or do I still have to go through some complicated process in order to convince the cloud that the 14,500+ unflagged emails don't then need to be "updated" to flagged status?
2) More importantly, will the cloud still sync properly so that I still get all of the emails that came since last night? I'm fine if the absence of the more recent emails from the "new" (actually older TM) mailboxes is interpreted as though they've been deleted, since my preferences are set to keep deleted email on the server for a month. But it would be a problem if those emails simply disappear into the ether.
3) Does anyone have any idea what might have caused the random flagging in the first place and/or suggestions for keeping it from happening in the future?
I remember vaguely that in the early days of Time Machine, restoring iCloud mailboxes was a complicated process in order to trick the cloud into accepting the Time Machine backup as the latest and greatest version. I take it that's no longer such a tricky proposition nowadays, since a search of Apple's knowledge base yielded little information on it. I'd appreciate some confirmation on that, however, so I know what to expect after the restore.
Thanks!
I'm going to try cross-posting this issue in both the iCloud and Time Machine forums since it's some of both. Apologies in advance if that causes confusion.

Answer 1

I set up an admin account for myself, logged on to it, and then followed the procedure in the help file to delete his account, saving it as a .dmg file.  Then, when he asked for his old emails, I followed the procedure in the help file to restore a deleted user account and copied the contents of the .dmg into it.
I'm not entirely confident I got the restoration sequence right, since I find the order of steps in the help file confusing. But everything except the Mail data seems to be recovered.
Another source of trouble may be the email account settings:  when I opened Mail under his log-on, there were no accounts set up: I recreated them using his email address and password, but Mail may well be treating these as new accounts, rather than re-opened old accounts.
Thanks, John