[KBTKaiser]

Spoiler:

Actually, the sakura branch would be left behind, but the only memory ricca would have of it is that a good friend gave it to her after the reset. So yes, partially a time paradox with the reset taking the Ricca end to connect to the DC1 storyline. The tree in present time DC3 is the 2nd tree, partially embedded with a system from Ricca's original system so that it would also act as a memory bank. In a sense, Ricca implemented the system during the reset, which maintained itself and eventually was transplanted to Hatsunejima by Ricca's hand. DC1 happens and the tree withers, Sakura takes a sample of Ricca's tree and develops the DC2 tree, presumably preserving the system in the withered tree as well when reintegrating the sample branch back into the withered system.

Now remember, the hidden system is keyed to those 6 people accessing the tree once again. So, the group touching the DC2 tree revives the system, presumably in its original state.