Nearly everything respawns, but on different timers.
Trees regrow from stumps quickly Stumped trees regrow after a week
Copper and silver nodes reapper after a week
Stones reappear after a week
If you hover over the tag item left behing it will show a timer - most times
To prevent respawn put up a ward, or a workbench.
Dirt, raised or lowered (dug out) does not respawn