I never really got to reading all of the earlier Sangetsusei comics in their entirety but I do remember there was that part with the three deciding to move to their current tree residence behind the Hakurei shrine. What was the reason for wanting to move into that other tree again? Also what became of their old tree home then? Is it still there sitting empty back the Forest of Magic? Perhaps they can still use it and have two bases of operations.

Monki said:

I never really got to reading all of the earlier Sangetsusei comics in their entirety but I do remember there was that part with the three deciding to move to their current tree residence behind the Hakurei shrine. What was the reason for wanting to move into that other tree again? Also what became of their old tree home then? Is it still there sitting empty back the Forest of Magic? Perhaps they can still use it and have two bases of operations.

The tree-house got destroyed because of a tornado.

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Rathurue said:

The tree-house got destroyed because of a tornado.

It didn't actually. In the end of one of the comics, Marisa revealed that the tree-house is still intact as some new fairy residents moved in not long after the Three Fairies of Light moved out and began pulling more pranks at the Hakurei Shrine.

Monki said:

I never really got to reading all of the earlier Sangetsusei comics in their entirety but I do remember there was that part with the three deciding to move to their current tree residence behind the Hakurei shrine. What was the reason for wanting to move into that other tree again? Also what became of their old tree home then? Is it still there sitting empty back the Forest of Magic? Perhaps they can still use it and have two bases of operations.

They moved to that tree because they wanted to not only have easier access to the Hakurei shrine and play more pranks but in hopes of one day inheriting the shrine(whether they mean from Reimu(aka becoming the owners) or the unknown Hakurei deity(becoming the enshrined resident) is unknown). They also originally planned to keep both houses to use as a base of operations but it seems they changed their mind and moved out of their old house completely(after Yukari fought them and let them keep the new tree to bring it back to life and prevent the Hakurei barrier from weakening). Marisa later revealed that their old tree home still exists in the forest of Magic and was eventually taken over by a different set of fairies(we don't know which fairies but it's possible that it could be Daiyousei and her greater fairy friends) not long after they moved out.