I did some quick testing and thrown tridents that have runes applied on them are very glitched.

Throwing a regular enchanted trident

It's colored orange for some reason

Orange thrown trident is colored correctly in this case

Dropping an orange trident reverts all colors to normal

Colors stay the same when picking the dropped orange trident

Dropping the regular trident and putting orange one in the off-hand recolors thrown tridents once again

Hello! Quark's moved to 1.18 now-- unfortunately, this means that (unless your bug is critical and/or game-breaking), we're closing support for issues filed for versions prior to it (e.g. Quark on 1.16).

If your issue still occurs on 1.18, or if your issue happens to be rather critical (e.g. consistently crashing the game with no other mods present), please leave another note or open a new issue. Thanks for your cooperation!

What causes this is fairly straightforward - the trident entity doesn't track the stack that sent it on the client.

Cannot reproduce the described issue in 1.16.5 r2.4-311, I assume this is due to commit 9fa5085 (correct me if I'm wrong), now the trident entity doesn't render the rune color at all.