I assume my "all to latest version" would have corrected this problem in the original installation, is that correct?
That's correct. The "all to latest" update is a fallback update that is used when the user changes one of the updated files.
Is there a kind of failsafe in that if things get changed within the users app install the updater will reset their version to the current version?
It doesn't reset their version, however it ensures they have all the latest update files. Let me give you two examples:
Example 1
3 Files in version 1.0: a.txt, b.txt, c.txtAll of the files are changed for version 2.0.
Before updating to 2.0, the user changes the contents of a.txt. Because the user changed the contents of an updated files, the user will be delivered the "all to latest" update instead of the patch "1.0 to 2.0".
Example 2
3 Files in version 1.0: a.txt, b.txt, c.txtOnly b.txt and c.txt are changed for version 2.0. a.txt is left unchanged.
Before updating to 2.0, the user changes the contents of a.txt. Because a.txt is not part of the update, the user will be delivered the "1.0 to 2.0" patch, and it will install perfectly fine. This is because wyUpdate doesn't worry about non-updated files even if they've been changed.
Can users update their version of the app and get a "reset" or later controlled version?
No, not yet. This ability will be added in the future. (It's one of the most popular requests).