Flash devices are treated similarly to hard drives. Writes are saved up and then done concurrently with reads, so if you're just playing tracks from a playlist they'll be buffered until the next time the flash chip is powered up.
If you're worried about wearing out the flash, this is not likely. With a 4KB block size, you would have to update bookmarks 1000 times to generate the same wear as copying a single 4MB file. You'd go through hundreds of lithium ion battery replacements before you'd generate the same amount of IO as just copying a reasonable sized music library.