The VPS shouldn't do anything to the avast, Mail Shield, Expert Settings, SSL account, settings either, so this seems to be an unfortunate coincidence.
The main thing is that in your email program email account settings you don't have any SSL/encryption enabled or avast can't scan the content. You could then safely delete the incorrect entries for those accounts in the Mail Shield, Expert Settings, SSL account and reboot that would recreate the SSL account entries.
What you don't say is ordinarily does your email account use SSL for POP3 and SMTP ?
As that would determine what ports the Mail Shield, Expert Settings, SSL account, would use.
On all of my POP3 account entries (5 of them) all are set to port 110 and none have been changed to port 995.
If your email account uses SSL ordinarily for POP3 then port 995 in the Mail Shield, Expert Settings, SSL account, settings would be correct.
- avast! 6.x: SSL Problems The Mail Shield may not scan some e-mails - see https://support.avast.com/index.php?_m=knowledgebase&_a=viewarticle&kbarticleid=842