@Incursor
It’s possible that Tirek’s magic drain involves his magic ‘latching onto’ a pony’s magic and dragging it back to him (which would make sense if his method relies on runes) - that would explain why the color of magic he absorbs is always the same.

Because of this, I will suggest that magic which is in active use has color - but not other magic. I’d theorize that the rainboom involves active magic pressing up against RD, too..

One thing that makes me reluctant to think the elements have been consistently transferring their magic to the element bearers: The tree of harmony NEEDS that magic. Surely it would notice, and take countermeasures to prevent the transfer? It’s practically a matter of self-preservation.

Pegasi magic normally is not visible in use, why is a separate discussion. But it is visible in high end uses like rainbooms, showing even normally invisible magic would be visible for high end uses.

Magic drains/transfers have been shown to involve visible/flashy magic, the one exception was the S8 finale which was due to it draining magic slowly over days, which wouldn’t have applied to the Elements breaking (an instant) unless they have been gradually transferred to them prior in line with my theory it happened before they broke.

@Incursor
That’s the thing. In use. Rainbow is surrounded by a flashy rainbow when she goes into a rainboom, but her wings aren’t constantly glowing. It could be that the elements are just massive stores of chemical magic, which doesn’t have access to emotions without a bearer. Magic without emotions is inert.

@ThePonyTheorist
Invisible? Maybe but that leads to the question why it would be despite their powers in use being the flashiest most visible thing in the series? Inactive? Wouldn’t their magic going to new vessels be/require they be active (every magic transfer of this magnitude has required such)?

The massive change was portrayed as their epiphany that they didn’t need the physical Elements to call upon their power which was in them. If the analysis aligns with the artistic intent of the work that sounds like a strong case for validity.

@Incursor
Now, I would say that’s an interesting position - but the image at the top of this ‘theory image’ is from the start of the beginning of the end, and the image at the bottom is from the same episode. Such a massive change suggests that the transfer happened inbetween those moments, surely?

Perhaps something about the nature of the elements’ magic made it invisible. Perhaps it was in an inactive state, for instance.

“Twilight’s Kingdom” showed such large amounts of magic being transferred is very bight and visible (see the princesses transferring their power to Twilight). So why didn’t we see this transfer here?

Hypothesis: they had already transferred their powers to the Mane Six, only being used to control them prior, before they were destroyed here.

As the Element of Magic still had power during “Equestria Grils”, the transfer most likely happed in “Twilight’s Kingdom” during the when they got Rainbow Power, which was bight and visible enough. It makes scenes as the Mane Six unlocking it required stand out act proving themselves their respective Elements and they had their magic stolen so they’d be uniquely ready as empty vessels save for what made them worthy. Plus is was the only source of magic Tirek hadn’t gotten to draw on until they got their magic back.

I mean Twilight did say they were the SPIRITS of Elements in the second episode of Season 1 so…

@Fwelin  
Check what happens with the actual gemstones. EVERYTHING channels through magic - Twilight does that now

So this is the fourth time or so the Elements were “destroyed” or whatnot and Twilight and co. made them more better-er with a STRONKER friendship…

If this were true, you’d think that all of them would get wavy manes, though.

@AC97  
The elements needed to be sure they were true friends.

Congrats OP. You get a wavy cookie.

@AC97
 
@starslayer159  
The elements were also colourless back then - it’s possible that they had lost their magic earlier. A better theory: It’s also important to note that the Tree of Harmony’s chamber (especially with Sombra in there as well) may be more magic-saturated than the abandoned castle of the two sisters - maybe the environment just made the formation of gemstones harder than just clinging to a nearby pony? The rocks which could have formed gems when exposed to raw magic could have done so long ago?

@starslayer159
 
Something, something, they didn’t embody them strongly enough then?

That’s a theory. I guess the only problem with it is why this didn’t happen when Nightmare Moon shattered the elements.

Makes sense to me.
 
And it’s a safe bet, that’s how twilight is going to look in the finale.

Makes sense.

Maybe doing this sort of thing is how you go from a “normal” alicorn to a Celestia and Luna type alicorn :D