FIRST !! Set your preferences to manual sync to make sure it will not do any further syncs with Evernote Cloud
Try signing out and quitting Evernote on your device and view your Notes using the EN Web client at Evernote.com (must be on a PC or Mac).
Check your Notes there, including the EN Trash.
Merging Notes does put the original Notes in the EN trash but does NOT permanently delete them.
To permanently delete the Notes in the trash requires user action (unless there is a bug).
Method 2 : Time Machine if you have a Mac
The key for restoring notes from a Time Machine or from another computer is to disconnect the computer from the internet. If you haven't open Evernote on your PC since you merge the notes, there is a chance you can restore them.
Disconnect your PC from the internet
Open Evernote on your PC
Locate the note and export them How to here
Once the notes are exported, connect your computer to the internet
Import the notes to your account
Best of luck!