OK. First off, since you are using Sierra, the V2 folder is useless. You can move it to the trash.
Follow the instructions below and see if it fixes your problem. Once completed, be sure to expand the On My Mac section to show the mailboxes.
If the first instructions of removing the container file does not work, try the second of reindexing mail. Please read very carefully and follow exactly all steps.
Remove Container file Mail:
Quit Mail.
In the Finder, select Go, then Go to Folder. Copy and paste the path below and hit GO:
~/Library/Containers/com.apple.mail
Move the whole com.apple.mail folder to the Trash, and open Mail and test. If all goes well, you can empty the trash. You may need to re create your user settings.
If the above doesn’t work, repeat the process with this folder:
~/Library/Containers/com.apple.MailServiceAgent
If there is a problem or you wish to restore the old file, first, Quit Mail.
Then open the Trash. Right click on the folder and choose Put Back from the menu.
Reindexing messages:
Quit Mail.
In the Finder menu, select Go, then Go to Folder and paste this path and hit Go:
~/Library/Mail/V4/MailData
In the Finder window that open to that folder in your user library, move all files with Envelope Index or ExternalUpdate to the trash. Open Mail and hit continue and let it finish. It may take a while if you have lots of email.