Here's what we do to ENSURE that the REMOTE SITE is ALWAYS COMPATIBLE with its LOCAL BACKUP.

1. We do a conventional, manual install of ZC on a remote server.
2. We add our custom template and all essential plugins (those we believe are essential).
3. We do all the necessary set-ups to "customise" the store (eg: meta_tags.php, english.php, header.php etc, etc...)
4. When we have everything ready (just prior to "launch"), we make a backup of the dbase and we FTP the entire folder/file structure to a local machine.

Then, when we make edits to files, we edit the LOCAL copy FIRST, and only then do we overwrite the file on the server.

We always edit the LOCAL copy FIRST... In this way we have an up-to-date file version on the LOACL machine AND the server.