In my installer script I have:
Section "Installer Section" SecInstaller
LogSet on
...
LogText "$APPDATA\MyDir"
SetOutPath "$APPDATA\MyDir"
File "SolutionTree.lic"
...
LogText "Installation complete."
SectionEnd
and the relevant part of the log:
...
C:\Users\{user}\AppData\Roaming\MyDir
CreateDirectory: "C:\Users\{user}\AppData\Roaming\MyDir" (1)
...
Meanwhile on the uninstaller I have:
Section "Uninstall" SecUninstaller
LogSet on
...
LogText "Deleting $APPDATA\MyDir\MyFile.txt"
Delete "$APPDATA\MyDir\MyFile.txt"
...
SectionEnd
and the relevant part of the log:
...
Deleting C:\ProgramData\MyDir\MyFile.txt
Delete: "C:\ProgramData\MyDir\MyFile.txt"
...
If I'm using $APPDATA in both the installer (an in the installer it points to the correct folder) why on the uninstaller it points to the wrong folder?
You are calling SetShellVarContext All in the uninstaller, this gives you the Machine/Common/All users version of $AppData.
You should try to use the same SetShellVarContext context in both the installer and uninstaller. If you are using RequestExecutionLevel Highest and supporting both per-user and machine installs, you need to save the state of the context somewhere so you can restore it in the uninstaller.
If you just need the user version of $AppData and don't care what the context is, use $UserAppData...