Random errors when promoting .xml file or when performing checkout operations.

All issues seen short after upgrading Harvest from 12.x to 13.x
 

Customer had checkedout files to same destination folder from a different Harvest versions.

Harvest 12.6 server performing checkouts to same destination folder as Harvest 13 could lead to this issue.
Each Harvest checkout will create its own harvest.sig file on destination folder and this could be the root problem.
An interesting test would be to use a new destination folder never used before and verify if it is ok. If checkout succeeds on new destination folders, then harvest.sig is most likely the issue here. 

The quickest way to fix the problem with the .sig file is to delete it and let Harvest create a new one during check out -.sig files are created by default if not present in the destination folder-. 
The only caution with this solution is that Harvest can no longer synchronize the folder and will check out all the contents of the folder rather than just the files to be synchronized. 
For more information, please see;
https://comm.support.ca.com/kb/i-understand-harvest-creates-a-file-harvestsig-during-check-out-is-it-possible-not-to-create-the-file/kb000047031