I think that performing a complete tower wipe, and starting with a clean slate, at the live launch of the rebalance would be a good idea.
Of course you would want to return all towers to their respective owners' inventories.
Reasons I think this is a good idea:
1) The game is grossly imbalanced right now and the current tower field situation reeks of this imbalance.
2) You might greatly improve the balance of the game, but the current situation is lopsided. All players (new, old, and returning) might enjoy the greater balance, but the old fields and side xp issues will be like walking in thick mud wearing brand new hiking shoes.
3) Speaking of RK1, currently you will see either a mountainous uphill battle or a ridiculously easy downhill stampede in terms of the side xp/tower field situation, depending on which side you choose. If you are trying to bring new players in and keep them, you don't want them to have to choose between an uphill battle or downhill stampede.
Anyway, this is my opinion. My apologies if this has been suggested elsewhere. Ciao.