Hi Brad,
All the pathways that were removed were automatically translated from human to cow and were not further curated. We agree that these are valuable, but our system for keeping them up to date was broken. In fact, many were based on a 2013 conversion. We are transitioning to a new and improved homology modeling system that will update the cow pathways each time its source human pathway is updated. A huge improvement! And the homology content will be exported as GMTs as well for important use cases like yours.
I will prioritize generating a new cow GMT for you with the latest converted content.
In the meantime, you can simply keep using the 20220110 GMT. The old content there wasn't being updated (by the old mechanism), so you are not missing anything by sticking with an older release.
I'll follow up with a handmade GMT for you soon.
- Alex