I’d also like to contribute bring attention to this bug. This doesn’t seem intentional
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Happens with tier 40 on my paladin as well: Holy Avenger and Seraphim will disappear from my bars if not selected.
It does not occur with tiers 15, 35, 45, and 50: Execution Sentence, Eye for an Eye, Justicar’s Vengeance, and Final Reckoning all remain on my bars when they are not selected.
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My pally friend is experiencing this issue as well.
In his experience (He has not done thorough testing):
Affected on Holy: Tiers: 15/25/40
Affected on Prot: Tiers: 25/40
Maybe someday…
Same problem here with spells and macros.
Bump. This needs a fix. I already have so many macros wasting space on them for something the game used to handle fine natively is annoying. It’s very annoying to swap specs then start a arena only to realize the button you are mashing is not on your bar and have to open your spell book mid PvP to re-add it for the 100th time.
This happens for sure with Light’s Hammer (holy paladin), Seraphim (all paladin specs), and Holy Avenger (all paladin specs)
I’m having this same problem on my shaman with the Stormkeeper talent, my druid with the affinities and wild charge/renewal, and on my paladin with seraphim. Just hoping for a blue post letting us know that blizzard is aware of this problem
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Turns out even Dwarves can be heroes 
Still happening as of August 14th. Very frustrating.
Once again, the following paladin talents, when not currently selected, disappear from my bars whenever I relog or enter an instance: Repentance, Blinding Light, Holy Avenger, and Seraphim. Those are all tiers 30 or 40 talents. This bug does NOT occur with active talents on tiers 15, 35, 45, or 50.
It happens with a fresh install of WoW with no add-ons.
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There was a bug i and another hunter friend found some time ago with Mend Pet not working in some way and we traced it down to having a full (8/8) set of the covenant armor. When you broke the 8/8 bonus, the problem went away. Do some tests with your bar with no covenant armor on.
The theory was that at some point in development they added some mend pet functionality to the 8/8 set bonus then removed it but didn’t undo any back-end mechanics associated with it.
As a Priest, this has been happening to me consistently with Shining Force (lvl 35 talent), and Inner Light and Shadow (PVP talent).
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I tested this on an alt level 50 paladin and the bug occurs with the same talents.
bump affinity spells disappearing after every different instance I go into
Still happens on live and now on the 9.1.5 PTR as well
Any chance we get this resolved in the PTR Blizz?
Still happening on every single toon for me. A full fix for this would be nice.
The talent tier macros are good if you don’t mind having all of the options for that tier in the exact same spot on your action bars, but for me that wasn’t enough.
I don’t like seeing/hearing the talent i want to use get re-added to an unused action bar every single time I swap to it for the first time after having been logged out. Some people can probably ignore that, but I am not one of those people.
But I found this addon that prevents that from happening completely, so if anyone else is like me in that regard, you will probably like it. I can’t link it but you can find it on curseforge, its name is DisableAutoAddSpells.
Bump because its sadly still happening in 9.1.5 
Why is this issue still happening? Extremely annoying when switching talents for PvE/PvP. Using a conditional macro (below) does nothing and the power is still added to my hotbar when switching.
#showtooltip
/cast [talent:5/1] Cone of Cold
/cast [talent:5/2] Cone of Cold
/cast [@player] [talent:5/3] Ring of FrostStill happening as of Nov 25th, 2021
still happening