Preview does not save annotations

you mean to Save As? Ye, but the problem is that it does no save this way the annotations! Only if I Export the file into PDF, only then it does! But then I have to do this after every significant change. Very annoying!

the annotations are not visible although they are present, all of them, in the Inspector window. May be it is only the fact that they were present is recorded in the Inspector but not the annotations as such. Basically, when you save the file and quit and open it again, you see only may be 10% of them. If you do just a few annotations, you may have all of them, but if you do a lot of them (as I do), then most of them disappear.

This problem has been around for a very long time, may be 5 years back and is still not resolved/fixed by Apple. But may be there is a fix since the Inspector shows that they are there, but I cannot find hoe to make them visible. The only fix I found is to export the file into pdf. Then all annotations are kept but you cannot edit them and the Inspector becomes empty, so the annotations become the essence of the new pdf file, they are not something written "on top" anymore as when you write them.

Thanks, Grant, for trying to help :)

My version is 11.7.10 Big Sur. It is a bit difficult for me to update the system actually as I have a lot of things which may not work and it takes a lot of time to update everything (I have a lot of stuff from Linux). But I also have another Mac with the latest system, I will try to play with it to see if the problem persists.

OK, I have not tried your two suggestions, the one with the Safe mode is interesting , I'll try! With a new user ID, that I'll also try. Give me a bit of time and thanks for suggestions.

What happens with annotations: as I said, out of like 50 of them I can only see may be 5-10 when I open the file again. However, the Inspector shows ALL 50.

I tried to do the same on a different Mac I have and it worked, i.e. the many annotations I made were all saved correctly. This tells me that there is some incompatibility with the other software (mostly, Linux I suppose) although the other Mac also have a lot of Linux stuff.

In this sense I'd need an advise as to how to detect which other app (if any) may affect the work of Preview and how to find this out?

I tried to do the same on a different Mac I have and it worked, i.e. the many annotations I made were all saved correctly. This tells me that there is some incompatibility with the other software (mostly, Linux I suppose) although the other Mac also has a lot of Linux stuff.

In this sense I'd need an advise as to how to detect which other app (if any) may affect the work of Preview and how to find this out?

Or may be it is not Linux stuff, but something else? But the other Mac was set up exactly in the same way as my main Mac. The only difference is the OS, the Mac on which I have a problem has OS 11.7.10 (Big Sur) and the other one where it worked is 14.3.1 (Sonoma). It is possible that the problem was fixed in that new release and the one before that, I do not know, I have been having this problem over a very long time. It would actually be nice to know IF there WAS actually a problem which WAS fixed, or it is just me and my Mac.