It wouldn't have anything to do with Adobe Reader.
By default, print presets are saved in Adobe InDesign's InDesign Defaults file. When your preferences are restored (which can also happen when you install a plug-in for example), the file and your print presets are lost.
You need to manually export them. This is from Mike Witherell's excellent PDF on InDesign's presets: File > Print Presets > Define. Create the Print Preset, then use the Save button to save external copies of the print presets.
Search for *.prst files on Windows Search if you're on Windows or *.prst in Spotlight search if you're on a Mac and you'd find the location of the Print presets if they have been manually moved to somewhere else, i.e not using InDesign Print Presets panel to Save to a location. If you find the .prst files then from InDesign Print Presets panel load the files and your presets will be back.