Embedding HTML file in folio causes other indesign files to be embedded into article

For our upcoming issue we have the following files:
COVER_Apr.indd
COVER_horz.indd
Calendar_Apr.indd
Chef_Tournedos.indd
Home_hybrid.indd
Kristen_Campo.indd
List_April.indd
Look_Back.indd
Masthead_Apr.indd
Pam_Sherman_Touch.indd
Review_Lucano.indd
Shop_talk_ChicFeet.indd
Short_festival.indd
Showtime.indd
SotH_Fondue.indd
TOC_Apr.indd
Taste_Test_Caesar.indd
editors_letter.indd
editors_letter_embed.html
When adding editors_letter.indd to a folio, (which uses a web content overlay of editors_letter_embed.html) inside of it, it seems that the other indesign files are added inside the article causing it to be nearly 40Mb. (I can tell this is happening because when updating the article it says
Adding File ...TOC_Apr.indd
Adding File... Shop_talk_ChicFeed.indd
..etc
If I remove the web content overlay, it is much smaller. (The total folio size)

Made a subfolder inside current folder and it seems to NOT add the other files now.

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