Moving a file to an encrypted in Google Drive will not automatically encrypt the file. Boxcryptor is a client-side encryption solution, i.e. you must use the Boxcryptor apps which encrypt the files locally on your device before they are uploaded to Google.
On your iPhone, files must be stored in Google Drive using the Boxcryptor app, i.e. your scan app must be able to send the scanned PDF document to the Boxcryptor app instead of directly uploading it to Google. On Windows you must store your files in the Google Drive folder within the Boxcryptor drive (e.g. X:\Google Drive) so that Boxcryptor can do its work.