If by lost their containment you mean that they are exposed circuit boards with the USB connector soldered onto the end, I would be concerned that either electrical tape or heatshrink tubing does not provide sufficient mechanical strength and that they will eventually become damaged.
Instead I would take some thin transparent plastic sheeting, like you find on store shelf product blister packs, a flat section of it, cut and fold it up into the appropriate rectangular box shape, seal the seams with transparent tape (temporarily), set this up on end so the USB connector sticks out the top the appropriate amount, and fill the voids with clear epoxy making sure not to get any on or into the USB connector. It might be easier to fill the container half way then slowly insert the flash drive down into it.
If you are careful pouring the epoxy in and use a slow set type, you can manage to avoid the formation of many bubbles so the circuit board is reasonably visible still, or to some extent you can also take a needle and pull bubbles up to the surface to get rid of them.
Then again, larger and larger USB flash drives have become dirt cheap over the years, and faster too. It might not be worth the bother considering that you're in the US where they are plentiful, opposed to some 3rd world country.
