If you can still find the SNote folder in your phone storage, then it's still there, just missing the S Note to open the files.

If you cant find it, most likely you did a complete wipe on the internal storage. Then it's all gone, unless you back up or sync your notes to Samsung account or Evernote, which you can retrieve back just by downgrading to modified stock firmware.

The very same place you downloaded your omni ROM, xda forum. As long as its modified stock with Samsung features in it, it will have S Note app.

Not sure if there any complication downgrading from 4.4 to 4.1.2. Should be fine if downgrade to 4.3 modified stock ROM. Right chuahcs79?

for starter i'm advise you to download ARHD v19. its like the stock 4.1.2 firmware but with tweak. one of the best firmware and still using the old note 2 snote. you need it to get back all your note backup on samsung account. the one on 4.3 mod firmware are mostly using the new N3 snote and N3 snote cannot recover the old N2 snote.