Ignoring Pending changes submitted by job

I have a job triggered by changes to a Code folder which produces some DLL files (let's call the job BuildDLL).
These files are submitted into source control for distribution to other users.
This means that the job always shows as having Pending changes, even though the only submit was by the previous run of the job!

This has only become a problem now that I want to use the job as a Snapshot Dependency. As it is always one version behind the BuildDLL job runs every time.

So let's say the job syncs latest cl100, builds the dlls and submits them as cl101. The job was built against cl100 so shows 1 Pending change (cl101). When Snapshot Dependency invokes BuildDLL it is out of date because the latest cl is 101, whereas it should skip the job ideally.

I can't exclude the Binaries folder from checkout rules because I need the folder to be present to submit new versions. If it's relevant I'm using Perforce and Stream depot.

What's the best way to get around this?
E.g. can I manually update the build version stored against a build?