When I go to https://goo.gl/ and am signed into multiple accounts, I cannot switch accounts like I can with any other Google app.
Is there a way to at least control which account I will be let in as?
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Unfortunately, Google Multi-login doesn't work with all Google applications, as you've discovered.
Probably your best option to use goo.gl with multiple accounts is to use multiple browsers or, if your browser supports it, multiple profiles.