Okay so this is ACTUALLY fairly easy.
In the Sons data folder located in LocalLow are a gabajizitiliniglioln Json files for all the stuff the game watches.
Learn it, if you do this you might care about other.

Your best bet given folder names is chronology; just try to make the save you're editing the newest timestamp.
To get rid of trees, all you need do is find the WorldObjectLocatorManagerSaveData file, and make a decision; you can restore ALL trees by just deleting the file or overwriting it with one from a save where the trees you want to keep remain standing. (A great use of this would for example be to make a backup of your save before starting to deforest, clearcut the area you want, and then replace said file with the backup.)
A second option would be to scan the file for the ones specifically want to restore; they seem to be attached to insanely large Identifier codes, which I suppose makes sense given the island must have dozens of thousands of trees at minimum. To do this (Pure hypothetical; have not tested) I would suggest making a new save, and heading over to a still-standing tree; having opened the json in word, beforehand so as to compare. Chop the tree down, make a new save, and then scan the new save for a seemingly anomalous new text string. If successful, the neighboring strings should be the local trees already cut down, and it should be rather easy to delete a few at a time so as to maximize peace of mind.

Should you choose to delete the entire file or just all the tree strings, you will be rather likely to have some trees inside your structures. The best solution is to copy the construction as a backup. Chop the building trees down, save, and then move the construction file back over so as to replace potential damages., without trees.