I had similar issue. Some settings for my mods were saved, but not all. I've also moved my WOT from HDD to SSD. So here are the answers:
According to WOT Path:
You have to change RegEdit.exe entry. WOT ModPack settings are under the following path:
Computer\HKEY_LOCAL_MACHINE\SOFTWARE\WOW6432Node\Microsoft\Windows\CurrentVersion\Uninstall\Aslains_WoT_Modpack_Installer_is1
There's set of settings. I guess the one you're inserrested is is named "Inno Setup: App Path"
According to settings:
I've contacted Aslain on Polish forum and he told me it's not possible to back up all the settings. He suggested me to back them up and restore manually. It can work, but is not perfect. Settings are stored in JSON file and it's not always ordered in the same order. It makes it difficult to track settings changes. I've written a small program for updating that config with my fixed values, but now I think I'll rewrite, so that it'll merge my backed up config into the config used by WOT - the one that's updated each time ModPack is installed.
I'll place that application here when I write it, it should be soon.