Although WinMerge v2.16.0 x64 has already been installed on my PC, an exiting v2.14.0 is found and an update is recommended.
I just search the registry for abandon entries and found out that an old WinMerge v2.14.0 entry still existed,
pointing to the non-existing directory path C:\Program Files (x86)\WinMerge. After I've deleted this entry,
PatchMyPC worked as expected again.
"InstallLocation"="C:\\Program Files (x86)\\WinMerge\\"
Thanks for the update.