Just as a heads up, the bug with 0-level wizard spells not disappearing is tied to specific portfolios - if a spell existed as a 0-level wizard/witch/magus spell at some point in its lifetime, and you saved a portfolio during that period, but the spell is no longer set as a spell this character should get, they'll show that spell. This will even happen if the character isn't a Wizard/Witch/Magus.
Unfortunately, we don't currently have a way to have Hero Lab remove things that are no longer auto-added to all characters - the record of that auto-added thing stays in the portfolio.
Thinking about this, the last time we had this bug, it was for a spell that was mistakenly added to the Wizard 0 list - everything else about the spell was correct, but it shouldn't have been available for Wizards. Since the spell you've created is in a user file, there may be a solution available - try moving that .user file out of its normal directory, then close and re-open Hero Lab, and then try opening the affected characters. You'll get errors that it doesn't know what that spell is, but if you click through that warning, then change something about the character (like adding and deleting a space in the name), then save it, hopefully the spell will be gone the next time you open the character.
If this is about the paizo blog's new 0-level spells, I'll get those into the next update, and I'll add a mechanism to keep them from showing up in all spellbooks, so I'm afraid I'd recommend holding off on those until I can get official versions in that will function correctly.