Another common misconception: when you watch a thread, you only get an email for the first time someone answers and not for every single answer.
You will have to visit the forum again to get new notification emails.
The only thing that changed as part of 1.4 was the active user limit for watched content. This is not related to conversations.
If conversation emails aren't going out and you're sure they should be (based on config), that would imply that all mail is broken. If nothing changed, you may want to contact your host about it (or your SMTP provider, if you're using an external SMTP server). Alternatively, you could try changing mail to be sent via SMTP (though this isn't preferred).
Well the feedback was coming from staff who know how to use the forum. It was the moderator forum they were watching. Their email alerts stopped after the upgrade and they had to reset them. I've no idea how many of the regular membership it affects.
Is there a way I can run a query to jump start everyone's current settings without resetting them?
No, because nothing changed in the upgrade related to this. The closest change is that there is an option that only sends alerts/emails to people who have been active in the last 6 months by default; simply visiting the forum would be enough to avoid that (unless you have something else going wrong; you can confirm this by looking at the last activity time on the ACP user edit page).