I would like to know how Cikatro works. His card reads : During the End Phase you may choose 2 llicit upgrades equipped to friendly ships at range 0-1. If you do, you may exchange these upgrades. End of game: Return all llicit upgrades to their original ships. What does exchange mean, can a ship with Cioaking Device, Rigged Cargo Chute or Contraband Cybernetics who has spent their charges regen these charges and have unlimited uses.

No.

You pick a Firespray with a Cloaking Device with 1 charge spent, and a G1A with a Contraband Cybernetics with its charge unspent, and you activate Cikatro, and now the G1A has the Cloaking Device with one charge spent, and the Firespray has the Contraband Cybernetics, with the charge unspent.

If the Firespray has used the Cloaking Device and still has the token, it keeps it, and no longer has to roll to see if the oken must be spent each round (this is by far the most common use for Cikatro).

At the end of the game, the upgrades are swapped back, which is entirely to make the points costs of the ships not change for the purposes of scoring.

What would make you think the charges are regenerated? Nothing on his card says anything of the sort.

The charges are applied to the upgrade card itself, not to the ship. Wherever that card goes, the charges on it follows.
Its Force charges that are applied to the ship itself and not the card.