Certainly no 'expert' here, but I'd say that it will not hurt to use a semi-coarse emery cloth on the choke area, if it shows some minor discoloration type pitting. It takes a WHOLE LOT of effort to remove even a thousandth of an inch with wet or dry emery cloth in a slotted mandrel and I can say that from experience. Same applies for typical spring type hones, but you run the risk there of changing something that may or may not matter, predicated on how you run it and w/what as a lubricant. Generally speaking, 'Crisco' or any of the veggie shortenings will provide the best lube for aggressive [remember the term is relative] and best finish/correct cutting using a hone. Go easy, measure often and don't create a 'bell mouth', unless you want one. Some factory skeet chokes use them; Remington, for one, on their older fixed choke 1100 bbls. BTW, those same bbls. set many a record w/good shots using them.
Flex hones work well with the same suggested lubricant as listed above, but you lose some control using them. They would be fine, IMO, for a quick clean up of a dull surface or to provide a clean fresh surface in a dull cylinder or choke when no dimensional change is wished. I would not attempt to use one for choke enlargement, period.
Remember that YMMV, due to technique and lubrcants and hone type, so approach it with some caution and you are not likely to encounter any issues nor problems.
If you are really concerned, pattern it with the intended use load now and then again afterwards to verify what, if any, effect you have affected. You are not likely to get so much as point removed from the choke's constriction w/o some considerable effort. I say that from experience, but it is mine alone. Other's may have dif perspectives or experience.
