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