FM10 with DITA-FMx, SP 2010.
If I check out a topic that has a conref, and I don't select "Checkout all dependent files," then in DITA-FMx the conref is not shown (because Frame did not copy the conref'd file to the C:\users location). So I have to select "Checkout all dependent files" to work in DITA.
However, when I save and then check in the topic, and specify a new major or minor version, the conref'd topic is also versioned, even though it has not been altered or saved.
I t would be nice if dependent files were not versioned unless they'd been altered.
I'm still playing with this. I discovered that if you check out a file without checking out the dependents, you can right-click the file and select "Download dependents." This copies the dependent files to the c:\users area without checking them out. When you check the file in and version it, the dependents are not versioned. For what it's worth, the dependent file remains in the c:\users area indefinitely.
It occurs to me that, with a copy of the file remaining in the C:\users area, if another user updates the SharePoint file my local copy would not be updated, and I would be seeing a stale conref whenever I opened the referencing file. To get the latest conref'd file, I'd either have to check it out, or (possibly) re-select "Download Dependents" from the referencing file. (I don't know whether the latter would work -- I haven't tested it.)