It seems to me that the smudges perhaps have either one, or maybe from these two causes
1. abrasive scratching
2. exposure to an organic solvent.
Both are injurious to acrylic products, and so that cause ( or causees), needs to be found and eliminated.
You are right to consider replacing the airtights affected.
Press snap close acrylic airtight capsules, with reasonable care can be prized open, to release the coin. Re use of the airtight capsule after 3 or 4 times, will weaken the seal.
Press snap close acrylic capsules are OK, but
I prefer ex British Royal Mint screw
airtight capsules, which offer a more secure gas seal, as well a much more positive mechanical seal. They come in sizes related to the coin they originally protected.
My LCS regularly releases the original proof coins contained therein, and saves the capsules for re sale, at 50 Cents each.
For proof coin sets, it is common practice to house all coins in a single case. If the case is fogged or smudged, great care and patience is needed to remove such blemishes.
Ideally, the coins should be removed if possible, and the blemishes removed with a superfine cutting compound. This cutting compound can prove disastrous to proof coins, and that is why they should be removed. The cleaned acrylic case needs to absolutely perfectly clean, before the coins are placed back in the case.
Unfortunately some cases containing proof coins cannot be opened, because they are ultra sonically weld sealed, and so the case has to be polished with an ultra fine cutting compound, with the coins remaining in the case. Very difficult to hide your corrective polishing work.