Odpowiedź znalazłem w logach:
[1844,619] Starting the uninstallation process.
[1844,634] Running Exec filename: C:\WINDOWS\system32\sc.exe
[1844,634] Running Exec parameters: stop GSPrinterSvc
[1844,712] Process exit code: 0
[1844,712] Running Exec filename: C:\WINDOWS\system32\sc.exe
[1844,712] Running Exec parameters: delete GSPrinterSvc
[1844,775] Process exit code: 0
[1844,775] Running Exec filename: C:\WINDOWS\system32\sc.exe
[1844,775] Running Exec parameters: stop GSPrinterDbSvc
[1844,853] Process exit code: 1060
[1844,853] Running Exec filename: C:\WINDOWS\system32\sc.exe
[1844,853] Running Exec parameters: delete GSPrinterDbSvc
[1844,915] Process exit code: 1060
[1844,962] Deleting file: C:\ProgramData\Microsoft\Windows\Start Menu\Programs\My Program\Dezinstalacja aplikacji My Program.lnk
[1844,962] Deleting directory: C:\ProgramData\Microsoft\Windows\Start Menu\Programs\My Program
[1844,962] Deleting file: C:\Program Files (x86)\My Program\PrinterInformationUpdater.InstallLog
[1844,962] Deleting file: C:\Program Files (x86)\My Program\PrinterInformationUpdater.exe.config
[1844,962] Deleting file: C:\Program Files (x86)\My Program\PrinterInformationUpdater.exe
[1844,978] Deleting file: C:\Program Files (x86)\My Program\InstallUtil.InstallLog
[1844,978] Deleting directory: C:\Program Files (x86)\My Program
[1844,978] Failed to delete directory (145). Will retry later.
[1844,978] Deleting Uninstall data files.
[1845,009] Deleting directory: C:\Program Files (x86)\My Program
[1845,025] Uninstallation process succeeded.
[1845,025] Removed all? Yes
[1845,040] Need to restart Windows? No
[1845,619] Message box (OK):
Aplikacja My Program została usunięta z komputera.
[1804,769] User chose OK.
[1804,785] *** Uninstall exit code: 0
W tym miejscu po prostu przekłada usuwanie folderu na sam koniec po niepowodzeniu:
[1844,978] Failed to delete directory (145). Will retry later.
[1844,978] Deleting Uninstall data files.
[1845,009] Deleting directory: C:\Program Files (x86)\My Program
[1845,025] Uninstallation process succeeded.