This issue has been discussed here - GST Worksheet not reflecting correctly
I am in agreement with you that updating Manager can be a bit dangerous sometimes, which is why I only ever used the Desktop version and now the Server version. It was a factor (but not the only factor) in my not wanting to use the Cloud Version. I wanted to be able to control updates to prevent this precise problem occurring.
I would recommend locking the previous years because it does prevent accidental cloning mistakes for example where when you clone an invoice for last year to re-use this year and you forget to update the date. So locking does have it’s uses.
What I would recommend (which is what I do) - update far less frequently, but before you do, backup your data (if you are using desktop or server version), update on one machine and see if everything is as expected and if necessary revert back. So always make sure you have the previous install file as well as your backup. Which is basically what you are thinking of doing. I have long since come to the conclusion it is the only safe way.
Programming is difficult and unfortunately changes can have unintended effects, but I do feel that the developer tends to roll out major changes like this without proper testing and consultation with users before release with the result that a lot of people end up getting frustrated because their GST and VAT returns have suddenly all changed.
Apparently there is a newsletter which you can subscribe to which advises of updates like this. I think that I will subscribe to that so at least there is some warning, but I do think more than a newsletter is required as I have been Manager for five years and I have only bee made aware in the last few months of the existence of this newsletter which many people are updating Manager without any idea of how it will change their figures.