I talked to Turley and Asylum (the UO Fiddler devs). What they think is happening is that there is junk data and old demo data in art.mul that has no index in artidx.mul. So UO Fiddler ignores that data, and when UO Fiddler saves art.mul, it doesn't save the junk/demo data.
The new art.mul should be perfectly fine since the client doesn't use any of that junk/demo data anyway. So in a way, it's a feature. It's getting rid of junk/demo data that the client doesn't even use. (It's just not saving any of that unreadable data).
Other UO utilities don't display that junk/demo data either, for the same reason: without a corresponding index # they can't "see" it / read it. I am betting you'd have a similar result with something like TDV Mulpatcher for the same reasons (unless they specifically coded some kind of workaround to save that data, or are "appending" the new art being added in some way that doesn't affect the junk data).
For clarity can you please tell me which version of AoS it is and which version of UOFiddler are you using? Is it modified client? Original AoS art.mul are around 47-67 MB depending on patch.