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Are you saying the Apple Books pref file, or the PDF Expert prefs file?
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I just saw this thread and then checked my Mojave install. My pdfs from Books are opening in PDF Expert as they did previously. I did not do anything special to make that happen. I did upgrade from High Sierra vs. doing a from scratch install but nothing exotic.
akwarner, thank you for replying to thread. Man, this is frustrating.

I have wiped the main drive twice, Apple+Opt+R installed Mojave. THEN only installed PDF Expert. The only application not from Apple. Assigned PDF Expert to all pdfs. Put the pdf into Books, opened the pdf in Books, PREVIEW every time. I just don't understand this.
 
I just saw this thread and then checked my Mojave install. My pdfs from Books are opening in PDF Expert as they did previously. I did not do anything special to make that happen. I did upgrade from High Sierra vs. doing a from scratch install but nothing exotic.
Are you saying that PDFs stored in Mojave Books, when double clicked, ALWAYS Open in PDF Expert?
[doublepost=1540682051][/doublepost]I’ve just booted from the internet.
Wiped my main hard drive.
Installed only Mojave.
Then, only installed PDF Expert.

Opened PDF Expert, made a new test pdf To desktop
Apple + I, the pdf, assigned all PDFs to open w PDF EXPERT.
Drug into Books.

Double clicked the Books pdf.
OPENS IN PREVIEW.

What the hell am I doing wrong?
 
I don’t understand why, if I wiped my fusion drive, installed only Mojave + PDF Expert. Assigned PDFs opening. Rebooted. PDFs open from Books in PREVIEW ONLY. Anywhere else, PDF Expert.

Akwarner, I don’t recall, do you have a fusion drive?
 
Is your fusion drive a DIY fusion drive or stock from Apple?
Have you tried trashing the LaunchServices and QuarantineEvents .plist?

I did download PDF Expert to test and I am able to change my default app to whatever I want. Will the pdf open with your desired app outside of Books?
 
Stock fusion drive from Apple. I ran several terminal commands to completely wipe the launch services. I don’t think I touched the QuarantineEvents.plist though. I trash any plist file associated w Books App. So many that Books wouldn’t open. So I wiped HD and ran TimeMachine backup.

But I repeat. I wiped the fusion drive, booted from internet, installed Mojave & only PDF Expert. Assigned PDFs. No joy. Mojave Books will only view PDFs in PREVIEW here.

I really appreciate you experimenting w my issue. Thank you very much.
 
I don’t understand why, if I wiped my fusion drive, installed only Mojave + PDF Expert. Assigned PDFs opening. Rebooted. PDFs open from Books in PREVIEW ONLY. Anywhere else, PDF Expert.

Akwarner, I don’t recall, do you have a fusion drive?

I do not have a fusion drive. I am using only the builtin SSD in my MacBook Pro (2018).
 
There is a slight chance this will work...
Locate the folder that Books stores its PDFs.
Right-click on one of the PDFs.
Select "Open With..."
PDF Expert should be in the resulting list, select it and tick "always open with this application"
OK
Now see if Books uses PDF EXpert to open the PDF
If it does work you can change all PDFs in that folder by select the original Pdf file in Finder again then choosing File Info, Open With and as above.
I think this method changes defaults in Launch Services.
I dont have access to my Mojave Mac for a few days so cannot test this but akwarner's experience suggests that the defaults can be carried over from High Sierra.
 
There is a slight chance this will work...
Locate the folder that Books stores its PDFs.

Now that is a great suggestion. I deleted ALL pdfs in Mojave Books. Keep them on the desktop now. THEN put one pdf into Mojave Books. Did a search for this pdf. The path is: User/Library/Mobile Documents/Books/Books/"Target" PDF.

Now, if you can get to it, or your own pdf in Mojave Books, tell me how. I have searched all weekend. Talked w Apple Tech and a Senior Tech. They have no idea.
 
Now that is a great suggestion. I deleted ALL pdfs in Mojave Books. Keep them on the desktop now. THEN put one pdf into Mojave Books. Did a search for this pdf. The path is: User/Library/Mobile Documents/Books/Books/"Target" PDF.

Now, if you can get to it, or your own pdf in Mojave Books, tell me how. I have searched all weekend. Talked w Apple Tech and a Senior Tech. They have no idea.

No luck! I dragged a PDF file into Books and double-clicked to open it and Books used Preview, as expected. I closed it then used Finder to edit the "Open with" preference for that PDF file (via Get Info) to another PDF viewer. Checked this this worked from Finder then went to Books and tried again. Books still used Preview.
Unlike you, I don't see any files in the Mobile Documents folder (but I haven't downloaded any PDFs from the Books app). Interestingly after I close the file it does not show in Preview's recent files list. This hints that Books has some special link to Preview that uses its viewer without tracking. This may be why it does not use user-set file preferences when opening PDF files. But this is speculation!
 
There is nothing visible in my Mobile Documents folder. But using the app Find Any File I found the books/books/ pathway but I have no idea how to get to it, or if it would even allow the change in Preview.

However, I am glad that I am not alone in facing the opening pdfs in Preview.
 
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