(1) I'm not suggesting you DO anything different, just proposing wording that might alleviate what seems to be some confusion on the part of users when they see the warning, so I don't see where any danger comes in there.
(2) If you're going to make one of these high-impact changes that requires a switch to program mode, rewrite the config and program, and restart, how ELSE can you do it but by doing that? Are you suggesting it would be better to do a reload first, leaving the PLC in program mode, then require an explicit switch by the engineer from program to run mode?
I guess I'm not following your last comment.