Could you please go to the following location on your system, and check whether your presets are present on your machine or not:
/Library/Application Support/Adobe/Adobe PDF/Settings
Also, is there any other Adobe application that is installed on your system, like Illustrator? If yes, could you please check if your presets are shown in those applications or not.
An error occurred while saving the commentAnnika Kappenstein commented
Thank you for your response. My custom preset files are not present on my machine at /Library/Application Support/Adobe/Adobe PDF/Settings. They do show up in Illustrator, but only after I restored the files from a time-machine backup.