From a Jesuit priest…
Father, I commend you for asking. Thank you. You are right to wonder about the use of the purificator for particles of the Eucharist in a ciboria. For the life of me I cannot figure out how any priest could think it is a good idea to use a purificator to wipe out a ciborium… unless they don’t believe that those particles are Eucharist.
No. Do not use the purificator. Use your index finger to move as much as you can out of the ciborium into the chalice. Then, when you purify your fingers, purify them over the ciborium and then pour the contents from the ciborium into the chalice.
Here is a helpful little video, in which I go through the procedure with some incidental remarks.