Light user of PS. Have been using and learning with no issues until today. Started to have a lot of problems today. Biggest issue I am having is getting a Program Error after I work on a layered PDF file, save it and then try to re-open. I am getting the Program Error 100% of the time when I edit and save. I tried reinstalling CC 2017 after updating to CC 2018 today, and still can't open the file on either version. I can open the PDF under default viewer but can no longer open within PS to continue editing. I also deleted the preferences at startup. All of this happened AFTER I lost all the files because PS was saying no data existed in the files...I restored the earlier versions edited on my cloud drive.
You probably shouldn't be thinking in terms of a 'layered PDF' file. Your layered master document, the one that you edit and update, should be saved as a PSD file. Save it to PDF for final use, but definitely not as a means to store the document for future editing.
Out of interest, why are you using PDF, and which preset are you using? PDF with the High Quality Print setting, is excellent for sending to be printed, or for viewing. Unfortunately Photoshop is not able to save PDF files with hyperlinks. InDesign, or MS Publisher or Word are able to do that.
PDF is how the files were sent over from another person. They sent with the ability to edit. Using High Quality Print Setting. I went back into a recovered file last night, saved as PDF without need to maintain PS editing and once I saved and closed I could not open it again in PS. Gave me the same program error.
Never had this happen before with a PDF. Not an expert at all with this, but I use occasionally to make minor changes/edits sometimes.