When you update to MP1 for ITMS SP2, copy file packages are lost. The tasks still exist and the entries in the DB still exist, but the packages are gone and multiple errors appear in the log viewer related to trying to find the packages.
This can be seen by verifying the contents of the Task Handler\CopyFiles folder. The GUID folders are present (possibly - they are actually re-created) but there will be no contents in them.
Additional custom content has also been lost. This includes custom unattend files, and potentially imported SOI files on site servers.
The upgrade of site server components appears to also perform an uninstall at some point, removing some content completely before trying to rebuild. Some folders like "images" are maintained, but many others are lost.
There is a solution, and a prevention.
Prevention: Backup the Task Handler folder prior to upgrading. This is actually a best practice for all upgrades relative to the 7.0/7.1 versions of DS, including moving to 7.5.
Solution: If you find yourself with deleted packages, you will have to re-add the files. Modify the copy files packages you have, re-point to the files, and re-save the package. This will re-generate the packages. Look to a backup of the files either on another site server, or in a backup that should have been performed on the NS and Site Servers prior to upgrading. Additionally, on the NS, files added under NSCap manually should be backed up (which would include custom Unattend files).