I have seen this warning a few times, however my circumstances did not cause me to probe deeper about the intended meaning. Until now.
One interpretation: ALL results from EVERY previous Processing Step (1, 2, 3) will be overwritten.
Another interpretation: (after checking, for example, only Step 3 after there was a problem with Step 3) ONLY the results from the checked Processing Step will be overwritten.
The ambiguity is in “the process”. Which “process”? Any of the three Steps? All of the Steps from the start of processing for the project?
There’s probably an answer somewhere in the documentation or on the community forum, however I could not find clarification.