If I remove all affiliations from a character with a stamped affiliation, is he still considered an affiliated character for the sake of effects? Or is he now considered an unaffiliated character until my removal effect goes away?

No he is not. He is considered unaffiliated since he has no affiliations.

The affiliation would be gone until the "remove affiliation" modifier is no longer in effect.

Edit: Beat to the punch. Next time I'll post my answer before stepping away from the computer.

By "Stamped" do you mean printed on the card?

If so the card is not considered affiliated for effects.

However the card is still considered to have the "printed affiliations" that are printed on it so you could use say a resource point from Conjuration to recruit detective chimp from your hand, even if he somehow loses the shadowpact affiliation (or now instead has the crisis affiliation, because you control a crisis on infinite earths).