I tried numerous things to resolve this issue, but in the end, the only thing that helped was rebuilding the Swiftfile index, which can be done in your HCL Notes “Preferences” menu (open your mail database and navigate to “More –> Preferences –> Mail –> Swiftfile –> Rebuild index )” as displayed in the screenshots bellow:
After rebuilding the index, the issue hasn’t occured again and HCL Notes Swiftfile was working as expected.