This actually only happened after an e-mail server ran out of space due to run away log files.  Normal Desktop clients were not affected.   It appeared to be a bug in K9 mail but even reinstalling/wiping all settings did not fix it (read e-mails would still not reappear).

This is moreso a bug in Dovecot where it probably messes up the index files.

How do you fix this in Dovecot/your e-mail server?

You need to delete the dovecot index and related files so they can be rebuilt.  Note if you have a lot of e-mails and a Desktop client this will force it to redownload all e-mails (possibly thousands or more for some users).  But it is the only way I could fix the issue in my K9 Mail Android client.

cd /var/spool/mail/yourdomain/youraccount/Maildir/.yourfolder

#Backup dovecot files

mkdir 00-dovecotbk

#delete dovecot files

rm -rf dovecot.*

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