Whenever I rejoin a map, which is often needed because the minimap randomly decides to disappear, all effects from my spheres are lost. This means that, after setting up and rejoining, my Poison Dart Towers and Frosties are reduced to about 50% of their range, which completely destroys my build and wastes a lot of my time. This also counts for squire walls, which are drastically reduced in health, skeletal archers, which lose a lot of their range and probably for freeze effects on proton beams, but I don't have EV2 (yet), so i can't confirm that.
Its an old issue. Gear passives are also removed and don't re-apply when the Builder rejoins the game. I believe that the only thing that stays with the Tower is builder stats.
Just to clarify, you're saying this happens when you join someone else's game, then leave that game back to the Outdoor HUB or Private Tavern, then rejoin the same game?