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OK, I see. It's a problem due to a discrepancy in the file structure created by MakeMKV. It doesn't create the SSIF files, and BD3D2MK3D need then to compute the required disc space. I have located the problem and fixed it. I will release a new version soon...
In the meantime, I don't know if MakeMKV can create an ISO, of if you can "burn" the file structure to an ISO with another program, but normally the SSIF files should be created during the creation of the 3D ISO. You should therefore be able to mount the ISO and process it without problem with BD3D2MK3D.
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