Did you get the file with OwlNest, using Tools/Download Firmware from Server?
It should have downloaded a file called
OwlWare-v10-pedal.bin, of size 254312 bytes.
If you've got another file (e.g. the .syx from GitHub), or if it has a different size, pls remove and download again, using OwlNest.
Once the upgrade is successful, the OWL should come up with a green LED. OwlNest will no longer connect unless you change the MIDI input and output in Application Settings: there should be an OWL-MIDI option if the device is recognised correctly.
Once on v10, have a look at Documentation / Getting Started
and pls start using OwlControl instead of OwlNest
Sorry if this all seems terribly complicated, but a lot of things changed with the last firmware. Once upgraded, everything will be much, much easier!