I don't believe there is any way to check in the checked out items after you've already upgraded the ALM version.
If, during the upgrade, you elected to create you Site Admin schema by "upgrading a copy of an existing schema", then you could uninstall the newer version of ALM and re-install the older version, telling the older version to connect to the existing schema. Then you could check in the items under the old version of the application, and go through the upgrade again.
Otherwise, I think all you can do is manually delete the records from the VC_* tables and lose the work in progress. Then you'll be able to upgrade the project(s).
If, during the upgrade, you elected to create you Site Admin schema by "upgrading a copy of an existing schema", then you could uninstall the newer version of ALM and re-install the older version, telling the older version to connect to the existing schema. Then you could check in the items under the old version of the application, and go through the upgrade again.
Otherwise, I think all you can do is manually delete the records from the VC_* tables and lose the work in progress. Then you'll be able to upgrade the project(s).
