I just finished talking with I think four people at Apple, trying to communicate this issue and get a solution, but it's looking like a bug that's been in Preview since 10.9?
I use the Annotate feature in Prevew sometimes to make comments and draw arrows on images. If you save the image with a format that supports Annotation metadata, (pdf and tiff, possibly png also?) you can then close the image, and open it again later and edit the annotations. (move an arrow, change a color, edit text, remove text, etc)
If however you save it in a format that does NOT support annotation metadata, as soon as you close the image, it "flattens" the annotations into the image, and its just pixels in the image and will no longer be selectable or editable the next time you open it.
I tried to do this today on my macbook, which I just updated recently to 10.9, and found that it was acting like I was opening an unsupported type when trying to edit metadata. The tiff was no more editable than the jpeg. If you go into the preferences for Preview, Annotations shows up under the PDF tab, as just one check box and edit box, for you to put in your name as author for the annotations you add. This is added as part of the metadata of course. If they had removed the feature to save annotations, this shouldn't BE here anymore.
Two of the reps I spoke with both told me that the Annotations feature "had been replaced" with some other thing that basically does the exact same thing. ("markup" or "adjustments" or something, I forget what they called it) but I couldn't find that name referenced anywhere in Preview, and even in 10.11 it was still referred to as "Annotations" in the preferences file.
The test I was doing for this was to open a tiff (or save a different image as a TIFF and reopen it) and then view the annotation tools. Select text, click in the image, and enter some text. Then if you select outside the image (zoom out if need be, so you get some grey area around the image you can click in to remove the text box's focus) you see you can move the cursor over the text box. It will change from a crosshair or arrow, to a hand, indicating the element is there and is draggable. You can move it.
So then save it. Even if you save it as jpeg, you can still edit it, as long as you keep the window open. But when you close it, it will get flattened if the type doesn't support annotation. Anyway, back on 10.8 preview I could open an annotated tiff and switch to anotation mode and then get the hand as I mouse-over the notes. They were editable, draggable, and removable. But that's not working on 10.9 and later regardless of what I try.
I was a bit frustrated by the last "senior adivsor" I spoke with. He had little experience with annotations, and wasn't aware that you could even save them and edit them later. I walked him through the process and then he tested it on his machine (10.11 I presume) and got the same results. From this, he declared that this was "expected behavior". I pointed out that five minutes ago he didn't even know what this was, how could he possibly be "expecting" anything? He conceeded that it was considered "expected" because it happened on his computer too. I asked if this was a bug in preview, and he said no this is 'expected behavior'. I asked him then, if it WAS a bug, wouldn't it be affecting him as well? So isn't "expected behavior" just another name for a bug? Are bugs to be "expected" instead of fixed, worked around, etc?
Anyway, I'd just like to hear back from some others to verify the issue and see if we can narrow down at which point it "broke". We argued a bit about that too, whether it was "broken" or "the feature had been removed". But I pointed out that even in 10.11, preview's prefs had the editbox for placing my name in the metadata for the annotations. This shouldn't be there if the annotations weren't being saved anymore. To that he actually agreed, and said I'd be hearing back from an engineer soon. He finally agreed that one way or another, something is wrong. Either that shouldn't be in prefs anymore (the annotation save functionality has been removed), or annotation saving is bugged.
I work for the Department of Redundancy Department