Well, if you get an AOR for either, just submit a webform to cancel the other one. But personally, I would let them get to my other application to avoid confusion. They will most likely send it back given they have another application in the system OR send another AOR. I will then inform IRCC, though I suspect for the Citizenship they will realize a duplicate application themselves.But aren’t you concerned about having two active applications at the same time?. I’m in the same situation as you having sent my paper application a few weeks ago, but I’m hesitant to reapply online because I’m not sure if it would be detrimental in the long run.
I did something similar for my PR Card application. It may be a different situation but it caused no issues tbh. I still have my old PR Card application showing as "Application Received" despite having my card with me. Anyways by the time they process it, my PR Card will be up for expiry