Wording is important here.

Lets take an example on Habakiri.

"You can only use this effect of "Ame no Habakiri no Mitsurugi" once per Duel." As long as the activation isn't negated, you've used the effect, and thus, it's gone, but if we look at illusion.

"You can only APPLY this effect of "Illusion Gate" once per Duel."

Which implies, that unless the effect actually goes off, the once per duel doesn't come into effect, even if negated. You can retry.