This is a continuation of a conversation from https://discussions.apple.com/message/23402788?ac_cid=tw123456#23402788
Summary answer: No scheme for avoiding erasing deleted files is perfect. Using cloning techniques, files deleted between archives will be lost. A lot of headroom on a Time Machine disk appears to be the most practical solution and it is not perfect.
Once a TM disk fills it will delete older logical-full weekly backups. So eventually if you delete a valuable photo it will disappear from the TM backup, but not for a long time if you maintain a goodly amount of headroom on the TM disk. I currently use only 20% of my backup space so it will go a long time before erasing deleted files. If I upgraded my TM disk to 3 TB I can't see the light at the end of the tunnel when it would erase deleted files.
You could use a CCC clone but then you would be reusing that hard drive periodically which is likely to erase the deleted files faster than using TM. It would be too expensive to use HDs for routine archives just to avoid erasing deleted files. Plus HDs are not a good archive media; they degrade on the shelf.
I see no practical scheme for routinely archiving the entire photo library. I do not think I have many photos and surprisingly it already adds up to 19 GB. That would require writing 4 DVDs regularly to keep the archive current. I am in the process of archiving my system onto optical disks now. It is a major effort that requires third party software (Toast 11 Titanium) and persistence. Optical archiving becomes increasingly impractical as the data to backup grows. I plan to archive the major folders in my system at most once a year because of the hassle of doing so. For these reasons very few people archive their photo library onto optical disk and even fewer do it regularly.
So you can't win. Eventually some deleted files will be erased from the backups or will not make it onto the archives.