I realise I am late to this conversation, but missing books shouldn’t cause parallel passages not to show up in the tool. If that happens, please report a bug. I can believe that funky \id lines would cause things not to work.
The dialog which defines which books are to be checked for parallelism is in the PP tool menu. It can be a different list of books to the project progress scope:
In Paratext 9.2 opening the Parallel Passages tool to (or navigating to) a book which is not currently included in parallel passage checking scope, should show a banner which looks like this:
Clicking the bold text in the orange banner adds this book to the list of books to be checked for parallel passages.
If the book is neither in project scope, nor selected for PP checking, I see this:
Clicking the bold text in the orange banner adds this book to the list of books to be checked for parallel passages and adds it to the overall project scope in Project Properties.
I am unable to prevent books which are part of a set of parallels from appearing in the PP tool. If a book is not created, not in project scope and/or not selected to be checked for parallelism, it still shows in the tool for me. The only difference is that verse references in books which aren’t in scope are shown in grey in the upper pane:
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