If you are on a Mac, press and hold the option key when clicking on the Help menu. Navigate to Troubleshooting > Recreate Full Text Search Index. This fixed the issue for me. Evernote Mac (Version 6.13.3 (455969 Direct)) was pulling 3 notes in the client, and 25 for the web-based version on my query. After recreating the index it matched exactly. As the author noted, it takes a bit of time depending on how many notes you have (I took a few minutes with 400 notes).