macosnotes.app
I am using my notes app on OSX 10.11.5 and iOS 8. For the most part, things are working, but I am noticing that many of my older notes are not searchable. When I type something in the search box, these older notes do not appear in search results even if there is a match. However, if I edit a note or create a new one, it is fully searchable.
My guess is that somehow the search indexes for my notes got corrupted. Is there any way to fix this or rebuild the indexes?
It appears this solution only works on 10.9 Mavericks…
Select a note, then press ⌘ cmd + F and type your search.
This will not work for 'pinned' notes that have been opened outside of the Notes app.
It's a bit difficult to diagnose this with the info you've given but from experience I've found that you are able to reliably "force an sync" with any sort of iCloud data by going to System Preferences and signing out + signing back in (it'll warn you about removing iCloud data from the device, etc.)
As said in the previous answer, make sure you are syncing your notes with iCloud and not with a) another provider (Google, Exchange) or b) not syncing at all (i.e., storing locally). Verify this on the iPhone in Settings > Notes > Accounts or on the Mac with System Preferences > Internet Accounts.
The best way to see what is actually being stored in iCloud is at its web app like you've been doing.
Best Answer
If your notes are in iCloud, make a local backup. Then in iCloud settings uncheck Notes. Your Notes will all be removed. Now turn Notes back on. They should all return and this force an index rebuild.