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Hydrogen determines the code block to execute via Atom's fold range, more precisely with the function editor.languageMode.rowRangeForCodeFoldAtBufferRow.
I'm abroad this week and haven't investigated yet but I'm afraid this is an issue within Atom itself. Maybe you could try if the code folding of Atom works as expected.
With this Python file:
Hydrogen: Run - with the cursor over
if True:
gives this output:No error when selecting Python code (not string) before Hydrogen: Run.
No error for
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