I think your case should be fine. I would just prepare some documents proving that you submitted and canceled the original (online) application, just in case they ask for an explanation. The documents can be 1) submission and payment confirmation, as well the 2) application withdrawal confirmation. https://www.cic.gc.ca/english/helpcentre/answer.asp?qnum=1181&top=15I had a study permit valid till Nov 2019. Graduated May 2019, immediately applied for PGWP, started work in June, then flagpoled in Aug.