You should be able to use ADF2DISK to rewrite your 12th disk. You will need the ADF for the 12th disk though. Beneath a Steel Sky is Freeware and if you are interested it's also available for free (but for the PC) at gog.com (legally). Also - from Revolution (the developer) web site "In August 2003, BASS was made available for free download and is now classed as freeware. The sources and resource files are available from
http://www.scummvm.org Using this new engine, BASS can be played on XP, MacOS, Linux, Amiga and pocketPC. Revolution extends its thanks to the SCUMMVM team for all their hard work in bringing the game back to life. Enjoy! "
By the sounds of it you can use the SCUMMVM engine for the Amiga to play it.