Is this an , IMAP account & you have configured your web mail with apple mail app ( vulture logo ) .
And , when you go to system preferences > internet accounts are these options checked .
And what have you installed in your system , is there any anti - virus , third party apps ? please reply , I have never seen or heard this issue and its a strange activity .
if you are using the stuff , please uninstall them .
After installing them you can rebuild the mails : Mail for Mac: Rebuild mailboxes
Or a second method is there : Take back of all mails in V4folder : Method for how to copy in V4 folder .
Click on go on top menu bar , hold option key click on > library > select mail folder > right click on mail there itself > click on copy mail > right click on extreme right hand side in column B , that is below persistence info.plist > click on paste item .
Entire mails are copied to V4 folder .
Go to the corrupted IMAP account , select it & click on minus sign it is deleted .
Configure new IMAP account , go to top menu bar ,file > import mail boxes > import data from > select apple mail > click on continue > select the back drop folder then choose new .
When new IMAP account is opened , a new folder with all mails will appear in the mail side bar .You can rename the folder .