DT Version: 1.12.2-0.9.4
MC Version: 1.12.2
Forge 14.23.5.2815

Something like this happened everywhere after the use of World Edit or /setblock command:

or like this:

Or, sometimes caused by structure generation:

Maybe add a check to see if the root block exists each time the tree updates?

This is caused by those block changes not properly updating the blocks near them. However, this could be an acceptable solution.

The update comes from the root block, not any of the branches. So this won't work. Setting/destroying the tree blocks with a setblock command is not a proper interaction and not supported by this mod.