Zotmoov can help with the temporary move of some linked files back into local Zotero storage (under Zotero\storage). Such that with file syncing turned ON, those files should be synced to Zotero servers and thence to the Zotero mobile app. And then Zotmoov can move the files back into your linked-files folder afterwards. Annotations are maintained (they are in the Zotero database, not the PDF file).

There is no problem with a hybrid file storage scheme ... most linked, some "stored". If you have Zotmoov set up to save new Connector files as linked files, that will continue unaffected.

The key "gotcha" is that you must have a sufficient online file storage quota (300mb free) for the file uploads. If you have been working with linked files, you have likely had file syncing turned OFF. And you could have accumulated a significant number of files under Zotero\storage without realizing it (eg webpage spapshots, note images). If so you might already be over your free online file storage quota when you turn file syncing ON.

As I mentioned, the fact that you are using linked and stored files does not change what is Zotero's inherently seamless access to annotations etc between desktop and mobile apps.

To do *both* transfers - from linked to stored and back - you can use Zotmoov's standard right-click menu options (including its equivalent of Zotero's Tools/Manage Attachments). But using its Custom Menus (see below) helps to streamline the process, including auto-adding a tag to keep track of which files are temporarily back in Zotero storage.

In Zotmoov's Advanced Options, you would create a Custom menu item named "Move to Zotero storage for iPad". Add the operations "Move From" and "Add Tag" (set to something like %temp_stored). Then add a second Custom menu item named "Move back to linked storage". Add the operations "Move To" (set to your linked-files folder) and "Remove Tag" (set to remove %temp_stored).
https://github.com/wileyyugioh/zotmoov/blob/master/docs/CUSTOM_MENUITEM_INFO.md
(NB the example shown there is the *opposite* to what you are doing. It is similar to Zotfile's old Send/Get From Tablet, which worked by creating linked files in a cloud folder temporarily, for access in an external PDF reader from that folder on a mobile device).

You could also designate a collection for these files while they are in this workflow pipeline - so they will be easy to find on your mobile device, and also make it easy to see which files need to be moved back into linked storage after use. That would be done in the usual way - dragging files to that collection, and then Remove From Collection later (those operations cannot be added in Zotmoov's custom menus).

I have a very similar set-up. I also use only linked pdfs, but given the size of my database, I haven't checked if there are snapshots and notes in the zotero storage that would be synchronized if I would switch the synching of attachments on.
So I thought that I might use a group : dragging the reference to a folder in the group (which makes the linked attachment disappear, attach the file (not linking)
-> the reference as well as the pdf turn up on the mobile Zotero on the tablet

But now I have a problem : after annotating the pdf, how do I get the annotations back to the original reference in the local database ?
I have tried the following :
in Zotero on the computer used "show file" from the reference in the group folder
copied the file into the usual folder of all my linked references (using windows file manager)
-------->> I loose all comments and highlights
tried dragging the whole reference from the group folder back to the local folder
-> nothing happens
tried dragging back to a different folder
-->> this creates the reference, including attachments,but again I again loose all highlights and comments (I think what actually happens is that the original reference in the original local folder is copied to the new folder locally, not using the reference in the group folder)

I extracted the comments while still in the group folder, then dragged the whole reference to the empty local folder ---> the note disappeares ....

Any idea how I can get my comments and highlights in the pdf from the group folder to a local folder ? In the group folder, the Zotmoov menu items are greyed out.

Because the method suggested by tim820 needs synchronisation of attachments of the whole local database : I have >6000 references with >5500 pdfs, and and even as most of them are linked, I still have had some "accidents". But these are not the problem. The problem are the automatic screenshots, some of which can be quite big and representing the whole article with all figures. Scanning storage, I have >500 *.html files, overall nearly 1Gb. And there seems to be no easy method to clear these out problery (except brute force deletion, with then many screenshot items in Zotero not linked to a file, I haven't gone there yet ;-). That's why using group libraries seemed to be the easy way, because I can tell Zotero to synchronize the pdfs of the group library only. The problem is getting the annotations back.

As far as I understand tim820's description (his first post " Such that with file synchronizing turned ON") and my understanding of Zoteros functioning, he suggests to switch file synching ON for the local database, but keep most pdfs as linked pdfs (so they will not synch) and only attach the files that one want's to synch. Unfortunately in my "old" database, I already have nearly 1Gb screenshots, which would all need to be synched if I switch attachment synching on. That's why what tim820 proposes is not an option for me (or I'm understanding something quite wrong)

Thanks, but this would try to synchronize all of the screenshots which are stored in My Library, so nearly 1Gb, so not possible for me.

Ok, if the "as needed" is really working this way, that would be great. But first I need to find a way to get rid of the larger screenshots. Trouble is that I can find the easy on the hard disk, but haven't found an easy way yet to figure out to which references they are linked ....