I’ve found the problem. I had placed an empty index.php file into a subdirectory folder under my main theme folder to prevent directory browsing on that folder.
The presence of this index.php was causing the wordpress file editor to assume it was the default index.php for my theme.
Renaming that file to home.php has resolved the problem and the file editor now properly loads my theme’s index.php file as the “Main Index Template“
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