I recently read this thread: http://www.hcrealms.com/forum/showthread.php?t=510920

And I find that the answer never really touched on the basic question itself.

Do the tokens (not the affects of the tokens) dissappear after a power is lost?

If so does that mean that simply outwitting a power can remove tokens?

And if not does that mean that if the power is regained through something like regeneration that one can go back to using the old tokens?

Tokens are only removed when something specifically tells you to remove them. And if the game effect that put them there is regained it will be able to take advantage of the old tokens.

From WIN (http://win.wizkids.com/bb/viewtopic.php?f=29&t=4676):

[C]Game effects remain a part of the game only as long as the character continues to possess or is able to use the power or ability. If a power or ability is lost (such as from a character being KO'd or being placed on the Sideline), all game effects of that power or ability immediately end, but any actions already in progress are resolved normally (including any effects of that action that resolve "after actions resolve"). Any effects with an ongoing duration such as effects that say “this turn”, or “until (X duration)” also immediately end. Tokens that are placed on characters or character cards for any reason are not considered a game effect.

A good example:

Proxima Midnight puts tracer tokens on opposing figures.

Even when she is KO'd, the tokens remain - they no longer do anything, but they remain.

Does that mean that tokens placed on opposing characters by someone like Iron Nail

won't transfer over to a replacement character?

From the rulebook on replacement characters:

Any ongoing effects that apply to the replaced character continue to affect the replacement character.

You transfer action tokens, unless you are specifically told not to do so. Why not these? Can you find anything that tells you they would be removed?

Not really no, but this bit in the rulebook:

Tokens assigned to the replaced character are assigned to the replacement character, including tokens for the action that placed them on the map, unless otherwise specified by that effect.

Seems to be referring to actions tokens rather than generic tokens but I appreciate it still says "tokens" and I have always played it so that all "tokens" are transferred. Just the clarification that says "tokens on cards" are not game effects made me think that tokens such as Iron nail's might not be "assigned" is all. I am assuming though "assigned" covers things such as placing a token on a character card.

I think that is an appropriate assumption.