I've been going around tagging for a month or so now, and this has been happening more and more frequently: tags that remove themselves.

Example: https://e621.net/post_tag_history/index?post_id=788203
Here I added some tags, and apparently automatically deleted some of which I'm certain that I didn't touch them. When I tried to copy and paste them back, it only allowed the tag back to return.

Is this related to tags being aliased and/or implicated?
And if this occurs again in the future, should I just let it be and leave them off the image?

Yes, these are cases of aliases (hi-angle_shot to High-angle_view and horsecock to equine_penis). generally when a tag is aliased, existing instances are usually recorded as though changed by the next user to edit the picture. It's perfectly normal.

HotUnderTheCollar said:
When I tried to copy and paste them back, it only allowed the tag back to return.

The back was being aliased to invalid_tag when you made that edit, it was a coincidence that it ended up back on the image (it should have added invalid_tag). Sometimes the system acts funny like that (which is why I always approve them twice :V).

HotUnderTheCollar said:
And if this occurs again in the future, should I just let it be and leave them off the image?

I don't want to say you can't, but it's pointless since the system will just remove them again.

If you are confused about a particular tag you can always check their respective wiki for a quick peak at possible aliases (horsecock, back).

Righty dokey.