Updated file saved (twice) to SecureAccess protected directories but only old files are there

Did you Safely Eject the flash drive when you were done?  If not it is possible the file was still in RAM to be written.

when I was finished with my editing, I used file>save in the notepad window. Now I’m wondering whether that maybe doesn’t communicate with SecureAccess.

You can not use an app to write to the vault. You save the file on a writable drive, hard drive or the flash drive, then use SecureAccess to write it to the vault.