Perhaps only incidental to the OP, but related nonetheless, this is another reason why, when producing backups, Scrivener should timestamp the project’s .scriv folder as well as the project’s .scrivx file, with the same timestamps, identifying them all as a unique set, distinct from the source project. (It appears that the manual backup option to not zip somewhat does this, in that it timestamps the unzipped folder. That concept and approach should be applied to all backup processes, so that all bak containers, top level project folders, and also the scrivx files themselves have the the same timestamp in the same format appended to the base project name.)
This would make working with baks easier and safer, would make the accidental overwriting of projects much less likely, and probably reduce certain common support issues (though not the OP issue in this case.)