I understand that when doing lua-based file writing and LJM-based reading of said files, the LJM app needs to set the FILE_IO_LUA_SWITCH_FILE bit to 1 in order to tell the lua app that it needs to switch files, which is watching this bit via LJ.CheckFileFlag(). But what does LJ.ClearFileFlag() do? Is there a bit somewhere that it flips that is then readable by the LJM app to confirm that it's safe for it to read the first file?
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That's correct. The FILE_IO_LUA_SWITCH_FILE register is readable and writable. After writing a 1 to that register CheckFileFlag will return 1 until ClearFileFlag is called. At which point both the register and the CheckFileFlag function will return 0.