Very cool article!
One thing to note, I've seen bugs in LisaEm where the linker throws either a bus error or "Bad Intrin Instruction" error, it may be possible to use LPW in a limited fashion, but you'll likely run into this at some point. A real Lisa would help in your efforts - at least until I find a fix for it, or you could use IDLE.
I do not have those supplement disks, but perhaps the tags can be regenerated. The tags are important for booting LOS - the boot ROM and the boot sector absolutely requires tags, but theoretically it should be possible to regenerate the tags for normal files as what they are, are just volume id, next/previous and file id values, all of which are available elsewhere.
The Lisa file system uses inode like blocks that, unlike unix, also contain file names. The file id is the same as the block id of these inodes offset by the start of the volume (I think the boot blocks - that is file id bbbb might be outside the file system I don't recall off the top of my head). But basically if you find the thing that looks like an inode for a specific file, say that's block # 100 and the first 30 blocks are the boot loader, then the file id should be 70. These values are just examples and have little basis in reality, but for illustration purposes.
The inode like block also has a list of the blocks in the files, I think they're pairs of words indicating a start/stop for a run, also offset to the start of the file system's first actual block. So then, with that you can then set the file id tag on each of those to the inode block #, and then the previous/next as well...
I should be able to whip up some code using libdc42 to be able to resurrect the lost tags from the inodes as described above, but I'm currently swamped with a ton of work related projects which is why it's taking so long to port the old LisaList archive here.
If they're actual Disk Copy 6 format file, what happens when you restore the Disk Copy 6 images to actual floppies, then reimage them to dc42 format? If they were made as Disk Copy 4 format from Disk Copy 6 they shouldn't need to be converted and might be readable in LPW despite the lack of tags. (Does anyone know the file format that native Disk Copy 6 uses?)
Does LPW reject them when you try?
I do see that bitsavers has Workshop Supplement 85 and not 86
here , which might or might not help.