Yeah how bonus xp works is a bit confusing. Its basically based on the level, not the amount. So if you have 1.5 levels of bonus xp, and you are on a level 47 character, that might a few hundred thousand bonus xp that would take you hours to burn through. If you swap to a level 1 botanist, you still have 1.5 levels of bonus xp, but it is only a thousand or so bonus xp. So you harvest for a few minutes, and get to level 4 almost immediately. Your bonus xp is burned through and gone.

Thats why when you switched back to your high level character it looked like it was just 'erased'.

Kinda' annoying, basically forces you to not play low level classes when you have rest xp to burn through, best way to avoid is either use up bonus xp before swapping, or try to get some alt classes to at least 20 or so, that way when you swap over while waiting on queue you don't burn through the bonus levels quite so fast.