If you need Illustrator files do the work in Illustrator. InDesign generated EPS files are not intended to be edited.
BTW, I’m not a big fan of placing INDD files into INDD, either. I tend to use PDFs for that.
[Referring to placing .indd files in InDesign documents] Why, then, are we given the option to do so?
I recently used this method to produce a 256-page photographic atlas with about 100 illustrations and close to 600 photomicrographs, all of which were labeled. I saved each figure as an .indd, each with layers for art, leader lines, and text. I had ZERO problems exporting to PDF and the book looks great. During the last project, however, the issue of crashing began, but even then it was less than 1% of the labeled figures.
Using PDFs is certainly viable, but then I'm opening the .indd file and overwriting a PDF every time there's an edit (and, wow, there are a lot of edits). That strikes me as slightly less streamlined. I guess I don't like things that are touted as features that don't work particularly well.
As for .eps generated from InDesign, I suspected as much. Thanks.