Quoted from silverballpaul:
the bonus units do not reset between players turns or at the start of a new game. They do however, reset and score through the saucer switches and the gobble hole.
Do you know for sure that they should? Looking at the schematic, the only way for the "Subtract Red/Yellow Bonus Unit" solenoids to fire is if the I "Red Bonus Hole"/J "Yellow Bonus Hole" relay fires. There's nothing in there about outholes or drains or resetting.
I have a '65 Gottlieb Paradise and some of the features take longer than a game to achieve so they are left as is between players and between games. They only reset once the feature is collected. It's kind of a neat twist on the rules where both players work to build up a bonus but only one player gets to collect it. It also draws in more games if the bonus is almost ready to be collected.
I vaguely recall that Bally Rocket III also leaves the lit planet unchanged between games because it takes a while to work through all of the planets.