If you last looked in your skillbook and had a filter open, e.g. looking only at green jewels (for JC, obviously) and afterwards start an upload of your characterdata all other patterns (red, blue, etc.) are deleted from the database.
Seems to me during the uploadphase you use a simple "first delete, then upload" approach -> at least that would yield the exact same result.
Please consider the following approach for tradeskills: a) if the skill is not there any more -> delete it, b) otherwise just expand it.

If this was the wrong spot to post it, feel free to move it to any place appropiate.

That's indeed the upload approach we are following. I think however, this bug should be considered to be in CP. CP should be able to detect you've got a filter active, and not delete the other stuff from its cache. Roster can't see the difference in CP data between a filter and someone forgetting and relearing the profession, relevelling it, and not getting all recipes.