This messagebox
This source file has changed. It no longer matches the version of the file used to build the application being debugged.
seems only to be appearing when I made a code change on the exact line where the breakpoint is.
I've found that I can just click the OK button. And when I then press F10 to actually execute the line that has changed, "Edit and Continue" kicks in and recompiles the code.
After that, the breakpoint is disabled though (it shows a yellow triangle with an exclamation mark):
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To re-enable it, you can just right-click the breakpoint and choose "Location...":
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which brings you to this dialog:
:
where you need to check the "Allow the source code to be different from the original version" checkbox. Click OK and your breakpoint will be enabled again.