Morning, how's Dundee? High winds shut the bridge all night last night, made things quite challenging for us!!
The Search query:
-[Stack Top]=[-1] [Stack Files]=[]
should show you the non-stack top files that are included in a stack.
Add the fields above as expression columns in a file pane, and you should see how the values work.
Note that this won't work if the stacks are collapsed. It can be made to work regardless, but I feel that going in to that at this point will only help to cloud the issue rather than help get the job done.
Some reading regarding stacks in MC, and how they work:
"are there tags or expressions functions to test stack membership?""[BUG] Rename, move & copy a stack (SOLVED)"Be careful with the delete dialogue too. If the stack is in a collapsed state, when you delete, the option to "also delete other stack members" is auto-selected, if the stack is expanded, I believe the option is deselected by default. Pay close attention to its state before pressing the delete key.
If you are in a view that list all of your audio of all file types, you can select all files, then use the right click, stacks menu to expand all stacks in one go. This will ensure nothing gets missed using the search query provided above.
-marko