If you’re in InCopy and you check in a story or an assignment, InCopy automatically saves edits to the individual ICML files on the server. So, unless someone overwrites those, the edits were made and saved. They’re not lost. They’re just not linked to in the InDesign file.
I do hear this complaint on occasion, and 95% of the time what happened was that InDesign is linking to a different ICML file (shared InCopy story) than the one the editor worked on. And that can occur for a number of reasons. You can check by following the links in the Links panel and make sure the ICML stories listed there are the ones the editor was working on. If not, Relink the stories as you would Relink a placed PSD file.
–AM
PS By the way, you say you were in InDesign, and you “checked out the assignments” which is not possible to do. I’m guessing some terminology confusion here. In InDesign, the Assignments panel lists Assignments and (linked) Stories. Assignments are filetypes that only InDesign can create and only InCopy can open. Stories … linked ICML files .. may be associated with an Assignment, or they may be “free agents” and appear in the Unassigned InCopy Content panel. I assume you mean you checked out the linked InCopy stories in the layout, and some/all/none may be part of an Assignment.
So I’m wondering why you checked out the stories in InDesign. The only reason to do would be if you wanted to edit the text in them. There’s no need to check out the stories if you want to just move them around or adjust their frames. It’s if you want to edit the contents, the text .. is that what you did? Or you may believe that’s part of the workflow, that InDesign users need to check out the InCopy stories when they work on a layout.