Was going to start a new thread on this, but will just bump yours: annotations has been broken in Preview since the High Sierra update (the older thread here: Re: preview.app pdf annotation bug). Had hoped the 10.13.3 update would have a new preview build, but it seems we've been on 10.0 (944.4) for a while now, and previous versions in High Sierra had the same problem.
My own annoyance with this — in addition to note annotations vanishing — is that every time I open a previously annotated pdf (whether it is highlighted, underlined, etc.), Preview decides the file has just been edited. Since I work with a large number of pdf files with notes and annotations, date modified is a handy way of organizing. Yes, I can tell Preview to revert back to previously saved version ("are you sure?" yes I'm sure), but I then have to close the file very quickly before the app becomes convinced it has just edited it again. And yes, I can use a file property editor to manually change the date modified, but the next time I open the file to read, it will be re-"edited" again.
Oh, also, if you drag a page from one pdf into another pdf — one of Preview's wonderfully handy features over the last years —, the "alien" page cannot be bookmarked. Try it! It often will bookmark one of the earlier pages in the document instead.
The work-around I've adopted is re-annotating and then print-saving as a new pdf, which fixes the annotations in stone, as it were (that is, they are no longer seen as annotations but permanent "fixtures"). Then reinsert my bookmarks from scratch. Then edit file properties to "real" modification date. Needless to say this is very time-consuming, laborious, and was entirely unnecessary before High Sierra.
