How To Prevent Losing Your Changes Before Upgrading
When upgrading, the only changes you will lose are are hard modified core files. By hard modifications we mean the actual core files and not soft modding through vQmod. Please note any third party files are not overwritten by upgrading.
The only way to prevent losing your hard modifications is to turn them into soft modifications by converting them to vQmods.
How To Transfer Your Modifications Into vMods
Download an unmodified zipped archive of LiteCart (same version as you are running). And unzip it on your local drive.
Use a file comparison software such as WinMerge
to compare the untouched set of files against your modified set of files.
Files that show conflicts are assumingly files you have modified. Create a vMod that performs the same changes and restore your modified files to the originals. See: How To Create a vMod
You are now good to go and can easily carry modifications between platform updates.
How To Adapt To Git
If you don't want to transfer your modifications into vQmods you have the option to adapt your project to Git. Using Git you can pull all LiteCart updates with a command and Git will merge them with your modified work.
See How To Adapt To Git
If none of the above will work for you
If you don't want to turn your mods into vMods, nore want to adapt to Git. Then hard manual work might be the only way for you.
Clone the production platform into an identical development platform. Both the files and the database. Make sure to update includes/config.inc.php.
Upgrade the development platform to the latest stable LiteCart version.
Use comparison software for files and folders like WinMerge
to compare the two platforms with eachother.
Transfer your hard modifications mods line by line from the production platform to the development.
Make sure everything in the development plaform is running fine.
Upgrade the production platform.
Copy your modified files from development to production.