I have had a similar problem to one posted in thread below.

I installed Microsoft Outlook 2013 and set up auto archive to save space on my 64GB SSD.  I moved the archive folder to my external hard drive and tried to set it up to save there.  I eventually ended up with 2 archive files.  And I deleted one.  Something obviously went wrong along the way

I ended up with last 3 months email in Outlook 2013, and then the previous 3 months email in an archive file.  I had ABSOLUTELY NO IDEA that doing this would have any impact on my 10000+ messages in online storage which I assumed would be safe.

Luckily until 2012 my emails were also forwarded to a alternative email provider but from 2012-May 2013 missing all emails