I don’t think the repo is corrupted, the problem could be with the parsing of Substitution Variable Datastore
check the following post to export the SV Datastore to XML file, if it gets exported successfully then try to open the XML in IE and see if it open fine
can you also go to DS MC , and try to execute the job from DS MC, do you see the section for overriding the substitution parameters, is it showing up or you get error on this page ?