If it happens, I assume, you can stop execution (and if no changes are made, run the app again, and they will still be all off?
If so, and if it happens again, stop, then "reset debugger" (from run menu). And run app.
Still wrong, or fixed?
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Also keep an eye, on editing while you are RUNNING. (and if this affects your issue)
In that case the debugger keeps a mapping, between the new line after your edit, and the line the code was on, when last compiled.
This map should (should!) be cleared on every run (assuming that all changed code was recompiled, and that the exe, and the editor will be in sync.
Editing while compiling, does not do that (and editing before the blue dots are loaded will also not). Sot in this 2 cases it will go wrong, but for one run only (as you edited, the next run will have a compile).