Quote:
Originally Posted by Andy North
Hello DoctorOhh, I am sorry if you interpreted my response as being disrespectful! I would be curious to know what made you feel like that...
Best wishes,
A
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I expect it was this statement (which was entirely unnecessary and comes across as snarky):
Quote:
Originally Posted by Andy North
HarryT, I appreciate your response but it would be even more useful if you had a suggestion to solve this problem, as I am 100% sure I am not the only person out of 7B people who is experiencing it! 
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As has been mentioned, there is no standard way of storing annotations for ebooks, hence, there currently isn't a method that's interoperable between reading systems (even epub to epub). If you want annotated copies that will work from system to system, I expect converting to PDF for annotating is your best option.
Marvin
You mentioned using Marvin 3. While Marvin doesn't automatically sync annotations at the moment, you can export annotations from Marvin to Marvin (as .marvinz file) and even backup these .marvinz files to iCloud, Dropbox, etc. To do this, while the ebook is open, tap in the middle to get the menu, go to Contents, Annotations, tap on the icon on the top right corner, Export (Marvin -> Marvin). You can send it to any app available in the share sheet. I regularly AirDrop Marvin annotations from iPad to iPhone and vice versa.
You can also export annotations to other formats (EPUB, PDF, HTML and CSV) but this export options only contains the highlighted text and won't be linked to the original EPUB. The process is the same as above except you select Export (multi-format).
Marvin also has a backup feature which backs up all your books, annotations, bookmarks and settings. I usually do a backup of my Marvin library every now and then which I send to Dropbox so I have backups on my computers.
Other iOS EPUB Readers
There are EPUB readers on iOS that do support automatic sync of annotations (and bookmarks and reading position). Three I know of are iBooks, Hyphen and MapleRead. iBooks and Hyphen both use iCloud for syncing. MapleRead requires creation of a free MaplePop account to sync data.
Thus far, Marvin is still my preferred iOS reader app so I'm not very familiar with the others. I've tried them, found they were missing some key features/options and went back to Marvin.