After some googling I found that this reason if caused by too many scheduled conferences by my Application Endpoint. My only problem is, how do I delete/remove currently stored scheduled conferences for my application endpoint, when the only access I have to my server is through PowerShell??
EDIT: Just found a command that actually could increase number of scheduled meetings per organizer (Set-CsUserServicesConfiguration -MaxScheduledMeetingsPerOrganizer 2000), but it didn't change the issue. I'm still receiving MaxConferencesExceeded error. Any ideas??
Use Get-CsUserServicesConfiguration to make sure the change has actually occurred, and/or setting it globally to make sure it has the correct context for your users.
I've also found with a large pool, it can take a while to kick in.
Have you tried republishing your Lync topology after making the change? A bit dramatic, but can help with Lync gets itself into a knot with changes.