The filestore.xml file did not exist in our scenario (for many, may be all users) and it was 13.2 that created the faulty 0 byte files. Interestingly Robert refers to the file as fileStorage.xml but it was filestore.xml that caused the problems - perhaps just a typo?
For the record, the filestore.xml that was copied over the 0 byte files / resolved the issue when reverting back to 13.0 contained this:
<?xml version="1.0" encoding="utf-8"?>
<FileStore>
<RootFolder>
<Folder>
<Name>Root Folder</Name>
</Folder>
</RootFolder>
</FileStore>
I am not sure if this impacted us because we have been using Smartermail since around v6 and the file store features was added in a more recent version and perhaps missed from our users created before it was introduced?