I have done some tests of KB4099950 on a Windows 7 x64 virtual machine.
Test #1: Created a SlotPersistentInfo registry key in an appropriate location as a test. File pci.sys on computer is v6.1.7601.17514. Ran KB4099950 catalog file windows6.1-kb4099950-x64_245d5aaf7d50587297825f9176be166c47ad10f7.msu. SlotPersistentInfo registry key was deleted (technically it was actually renamed).
Test #2: Created a SlotPersistentInfo registry key in an appropriate location as a test. File pci.sys on computer is v6.1.7601.17514. Installed KB4088878 and rebooted. SlotPersistentInfo registry key was still present, contrary to what the KB4088878 article implies would occur. Installing KB4088878 caused pci.sys to be v6.1.7601.24056. Ran KB4099950 catalog file windows6.1-kb4099950-x64_245d5aaf7d50587297825f9176be166c47ad10f7.msu. SlotPersistentInfo registry key was purposely not deleted according to the pciclearstalecache.txt log file, presumably because the version of pci.sys is too high.
Discussion: If the fix wasn’t successfully applied before installing KB4088881, KB4088875, or KB4088878, there perhaps is nothing that you can do to fix the issue except one of these:
1. Restore an image made prior to installation of KB4088881, KB4088875, or KB4088878.
2. (Speculation) Restore a system restore point made prior to installation of KB4088881, KB4088875, or KB4088878.
3. Fix manually.