If you go sheet metal duct instead, you will have to buy a lot of fittings, do a lot of cutting, sheet-metal screwing, taping, etc. Then, you will have to insulate the outside of the metal duct, with care to make the outer vapor barrier continuous.
Sounds like you're stuck with either not using the furnace (and ignoring the mice noises/damage) or doing the right thing with metal ducting.One duct company said that code requires that those be sheet metal and not flex duct.
I considered replacing it, but we simply do not use the furnace. I run it 10 minutes per month so that it won't feel neglected.
In the perhaps unlikely event that you sold the place, the inspector would point out that the crawl-space ducts didn't conform to code-- and you'd end up replacing them in a hurry or giving the buyer a retail-price discount. Maybe this is an opportunity to leisurely replace the flex ducts with metal, on your schedule and whenever you feel like working on it, and especially if you can get a good deal on sales or Craigslist "contractor extras". Replacing existing ductwork seems to be well within the capability of a homeowner with your skills & available time, although this time of year might be sucky weather to do it.
Besides a metal duct tastes yucky to field mice and rats.
Speaking of taste and mice-- your refrigerator water line and dishwasher supply lines are made of metal... right?