If I've got the donation machine to 999 will bombing for coins it relock the Stop Watch, or do unlocks stay unlocked?
As the Rebirth Wiki states:
When the amount of coins donated increases past 999, the machine will explode, dropping roughly 12 dimes and resetting the total to 0.
Nothing unlocked through donations will be lost if the amount of coins in the donation machine is reduced in any way. Thus once something is unlocked it can never be locked again.
Once something, shop or other, has been unlocked, it will never be "re-locked".
This does not only apply to the 999 cent barrier, but to the earlier ones as well (Blue/Red/Black Candle, etc..)