Rather than creating a 1-to-1 relationship between Obsidian vault MD files and Foundry Journal entries, give an option to create a vault folder as journal entry that contains multiple pages (the MD files). Place the Index entry, if created, as page 0 in the new journal.
This breaks a bit if the original Obsidian vault folder contains sub-folders itself. In that case, create the subfolder in Foundry, but place a single collated journal of entries in it.
As an option to the normal behavior:
Rather than creating a 1-to-1 relationship between Obsidian vault MD files and Foundry Journal entries, give an option to create a vault folder as journal entry that contains multiple pages (the MD files). Place the Index entry, if created, as page 0 in the new journal.
This breaks a bit if the original Obsidian vault folder contains sub-folders itself. In that case, create the subfolder in Foundry, but place a single collated journal of entries in it.