I got a 0 mana spellstone in the Dalaran Heist ,during the tavern, and when it upgrades, it loses it’s 0 mana value
To make sure this was a bug I made a deck with far sights and lesser sapphire spellstones and played against the innkeeper. I managed to pull a lesser sapphire spellstone from one of my far sights making it cost 4, and upgraded it all the way to greater sapphire spellstone and its cost remained 4, which makes me think that the bartender bonuses not remaining with the upgrades is indeed a bug.
It seems the buff considers itself created by the minion that it's attached to:
https://www.reddit.com/r/hearthstone/comments/bpoxcy/bartenders_give_a_minion_44_it_costs_2_more_does/
In a similar but less widely reported case, Spellstones don't seem to retain these discounts when they upgrade, even though they do retain normal cost modifiers (#874): https://us.forums.blizzard.com/en/hearthstone/t/0-mana-spellstone-becomes-7-mana-after-upgrading/5815
It seems the buff considers itself created by the minion that it's attached to:
It's possible there's some check to ensure that the buff cannot be attached to a different card ID.