Files Missing From iCloud
I use iCloud to save my Pixelmator files. I opened Pixelmator today to edit one and no files are there. I should have around 20. iCloud drive on my mac is empty. I have two apple ID's my original domain email and my .mac email. My Mac is logged in using my domain email and Pixelmator is checked to use iCloud. The iCloud panel in settings shows both my .mac & domain emails attached to it.When I login to icloud.com (using my .mac address), I don't see any of those Pixelmator files. When I go to restore deleted files under settings it shows none. If I log in to icloud using my domain email I see the files in iCloud. It is like my Mac is not seeing the iCloud files on my domain apple ID. Yet on on the control panel of icloud.com for my domain email it shows both my phone and my mac. BTW my phone only sees the .mac iCloud files.
So it seems like even though I have both email addresses tied to my iCloud my devices are not seeing both. Help!
MacBook Air, OS X Yosemite (10.10.5)