I Have an iPad and I purchased my wife one recently. We decided to utilize the same Apple ID.
after I copied all of my contents to hers, I deleted the notes from her iPad, and found out they were deleted from mine.
Is there some way I can retrieve them?
Thanks

Huge mistake using same AppleID. Change hers to something else and start over. You will confuse iTunes and syncing will have inpredictable results.

It is not a huge mistake to use the same apple Id and syncing should not be unpredictable, we just need to figure out what the OP actually did.

I have 4 devices sharing the same Id and syncing to the same library and have no problems having different or the same content on each device. You just have to setup each device correctly.

What the op might want to do is share an apple Id for store purchases but have separate ids for iCloud syncing.

If two devices share the same ID and notes via iCloud the notes are gone when deleted off both devices as they are in synch