You mean you want to encrypt a file which is already on your GoogleDrive?
Well, then you see a copy of this file also on your Boxcrxptor drive - but it's not encrypted.
Now, if you encrypt it, the file will get on GoogleDrive the .bc extension.
If you delete one of these file (on GoogleDrive or on the Boxcryptor drive), BOTH files will be removed.
Your original file is never encrypted, it's locally on your computer. So, if someone has physically access to your computer it can also access your files on GoogleDrive if you don't lock Boxcryptor or the PC.
Hope, I was able to clarify a little bit.