It depends on your policy. Encryption is "sticky" so for an encrypted file to become decrypted, you need to copy it somewhere where there's an explicit decrypt policy.
Save As creates a new file, so if you're creating it in a folder without an explicit encrypt policy, it will be stored as plain text, unless there's a file type policy in place causing all files of a given extension to be encrypted.
Save As won't decrypt the original file, nore can you "save as" over the top of the file you have open.
So yes, what you say is quite easy to explain in terms of policy settings.