Just wanted to add, that after you remove the package in question you might also need to check to see if it's listed in the list of packages in the following area and manually remove its listing:
Preferences>Package Settings>Package Control>Settings - User
In my instance, my trial period for "Sublimerge" had run out and I would get a popup every time I would start Sublime Text 2 saying:
"The package specified, Sublimerge, is not available"
I would have to close the event window out before being able to do anything in ST2.
But in my case, even after successfully removing the package through package control, I still received a event window popup message telling me "Sublimerge" wasn't available. This didn't make any sense as I had successfully removed the package.
It wasn't until I found this "auto_upgrade_last_run" file and manually removed the "Sublimerge" entry and saved my edit, did the message go away.