Separate the library entries from the media file
A combined file can appear as several episode entries after correct multi-episode naming. Selecting the second entry does not mean a second physical video exists. Kodi’s bookmark documentation provides a way to associate an episode with a position inside that shared file. This is useful when the second story begins after credits or a short introduction rather than exactly halfway through the running time.
Set the documented episode markers
The manual describes playing the combined item, pausing at the relevant beginning and opening the bookmark control in the playback display. Set an episode bookmark and choose the matching episode from the selection. Repeat at the next episode’s actual start. Use recognisable dialogue or a title sequence to check the position, and distinguish an ordinary personal bookmark from the episode-specific selection. These are navigation markers rather than exported edits of the media.
Read the whole-file progress limitation
Kodi warns that individual watched status is not automatically independent for sections of one file. Finishing the last episode can mark the represented episodes watched, while partial viewing can leave several entries in progress. Its documented Start from beginning choice uses the selected episode bookmark. Test the intended library entry and inspect the resulting progress instead of assuming that the interface has created separate episode histories. Keep that limitation in mind when different household members watch portions of the same combined file.
Questions, answered
Do episode bookmarks create independent video files?
No. They point into the shared file; the documented whole-file progress and watched-state limitations still matter.