If you search this forum for the "noimage" cheatcode, you may find some reflections on this theme. It is a principally important problem, but one reason why it doesn't seem to have attracted so much attention/action on Knoppix, is that disk writes to persistent store in practice don't happen all that often when there is an ample supply of RAM to use as cache.

There is really no principal difference between programs in the cloop and programs installed later when it comes to disk writes when a persistent store is in use, and whenever you update a program in the cloop, the new version is stored in the persistent store.

If you keep on issuing sync commands all the time, you force writing, but in general, disk writes may be fewer than you think, and because this is largely kernel stuff, nobody may have the exact answer about when Knoppix writes to disk.

I would also like to point out that the effective number of writes to a flash location is a random variable with a variance larger than we like (and the vendors tend to admit) So you are actually killing your usb by using it for anything that repeatedly writes to it. It just goes on so slowly that most won't notice, but every now and then the problem surfaces.