I need to fix a deployment...

...with a sledge hammer.

A number of revisions have been made by another party that I need to roll back for a client. Unfortunately, I don't have the last handful of builds the third party created. How do I go about uploading a patch that will put all the client's customers back on the right track?

You can just leave the version tabs empty for the versions you don't have in your possession. This just means wyBuild will build the full files (instead of patches) from these old bad versions to your latest fixed version.

Does that make sense?

So, in other words, just pick a version number I know is higher than his last release and continue on as normal, yes?

No. You need to add blank versions (the version number matches, but no files in it) for the botched releases.