Dreamcast-Talk.com

Yes of course I will keep you posted
I'm going to try it out. The only thing I am afraid of is that once burned it will have to refer not to a file but to an LBA value ...

Well I managed to move forward a bit by finding 2 softwares to do it but the end escapes me a little.

First there is the Darkfalz software called MultipleFileLBACopier.exe. It will allow you to create a script.txt file from a crc32.txt file.
Here's how to start:

- move crc32.exe,MultipleFileLBACopier.exe and newfile.exe to the folder containing the data (we will call it data) of the future game to be burned. Open a back window (cmd.exe), go to the data folder and write : crc32.exe folder1/*.* > folder1.txt
Do the same for the other folders (folder2.txt, ...,foldern.txt)
Finally, open folder1.txt and add at the end the contents of folder2.txt then that of folder3.txt, etc ...
You will have a single file containing the crc32 of all the files in the different folders of our data folder.

Launch the MultipleFileLBACopier.exe software and indicate the path of the crc32 and script files (a relative or absolute path is possible) then click generate. It will create a script.txt file for you containing all the redundant files. It will also create you a zero.bat file which will create empty files of all our identical files (except for one of course which will be the reference file). Launch zero.bat. Then the ISO patch does not seem to work.

So I found another tool that I have not yet fully understood, which can starts from the script that can be generated in MultipleFileLBACopier.exe if I understood correctly.

I am enclosing the 2 software for those who would like to test and find out how to finalize all of this.
For both there is a readme.txt file which gives a lot of information.

I think I'm on the right track but I get stuck on the end

I found this text file explaining the principle of re-linking redundant files by TuxTheWise

Okay there I found it
SMiTH had given the solution from the start
It was enough to use mkisofs.
Here is an example of a command to type:

mkisofs -duplicates-once -C 0,LBA_Value -V NAME_OF_GAME -l -o data.iso data

It automatically searches for duplicates and creates links for redundant files.
I tested Powerstone 2 in US version and JAP where there were a lot of common files.
The 2 games work wonderfully

Oh snap. Great detective work! Sorry for sending you off the beaten path. Now we know. One less thing, which is good lol