Extension filed online but return is through desktop program

I filed my extension on time in April 2022.  I was completing my tax return through the desktop version.  For some reason, it would not allow me to electronically file my extension through the desktop program.  So, I had to go to my TT online account and file it there.  It was successful and I made my payment.  Now when I go back into the desktop program to finalize my filing, it started with my federal refund of $0.  Is that correct?  It also wasn't showing my deductions I entered - again maybe because I filed the extension and paid estimated taxes?  I have added my additional deductions which is showing a refund...I am guessing a refund from what I already paid?  Do I just file like I would normally?