Recently I noticed that my VIP folders and Flagged folder have nothing in them more recent than Sept 2017. I have hundreds of emails from those VIPS with dates all the way up to today (May 2019) and about 100 flagged emails in my various inboxes.
I did a rebuild on all my inboxes yesterday and everything was back to normal. Then, today I opened mail and it's back to the way it was before rebuilding.
Not sure if this is coincidence or not, but inside my Library/Mail folder I see a V5 and a V2 folder. The V2 folder only contains a single file named Accounts.plist inside the folder Library/Mail/V2/MailData. The date on that file is 9/21/17, which is the same month in which the contents of my VIP folders end.
Any suggestions on what the problem is and how to fix?