Or just have it blindly attempt to delete the file before it tries to install it. I might suggest a mass delete option, but that would obviously be too dangerous (unless you included at least 2 "are you sure" prompts). I admit I'm not a coder, so I have no idea what it would take, or if any of this will work. But thanks for looking into it.
Not necessarily. It merely includes a python script to download it from CDN. If you kept your old copy, you might have one laying around that is 9.5 (957,440 bytes). Actually, you can download an older version with 3DNUS as well. The title ID is 0004013800000002. 9.5.0-22 is version 19216. 9.3.0-21 is version 18182. 9.0.0-20 is version 17120. Uncheck "Pack as .CIA". Look for a file named "00000040" and rename to firmware.bin. I would not go lower than 9.0, as it's likely not to work (some of these may not either). I was under the impression it was just the browser they patched. Oh well, can't hurt to try it. Hope that helps.
Updates are not legit CIAs (well, maybe the Streetpass Mii Plaza one that comes with the N3DS is, doesn't seem to be tied to the eShop, but aside from that, they're not). The only way to make them work in SysNAND is ticket.db injection. You can do that the manual way by decrypting the FAT16 partitions and using WinImage, or just wait for the rxTools update with working injection.