I thought about something similar for binary parsers. Here, too, there are often many different ways to express a certain structure. Most libraries (such as Exiv2 for PNG/JPEG/EPS/etc. metadata) perform the following procedure: First, they parse out all information they are interested in. Then the application modifies that structure. Then it has to be embedded back into to binary format (here the image). The latter step is a nasty type of merging. They go over the file, try to find places where to "safely" embed or replace parts, then serialize their stuff and try to put it there.
However, if the binary parser was lossless, all changes to the parsed structure would preverse the "trivia", so serializing is straight forward. And any potential issues could be handled on application level in the parsed structure, rather than by guesswork and heuristics during the merge phase.
The only problem could be large BLOBs, but those could easily be represented as position & offset in the original file, rather than as the actual binary data in memory. (assuming the file will not change in the meantime, but in that case there the "merging" approach is very dangerous, too.)