There is no checkin button or command! I opened up a case since I believed that this is a bug. There is already an article describing, that you need to create a new File to checkin the current one. See CS320314
The response from PTC was:
I discussed the possibility to patch Illustrate 6.1 with R&D but it turned out that it is not feasible as this specific issue became obsolete as we have introduced enhanced workflows and options to manually check-in and check-out files (from a workspace). This is an enhancement we cannot port it back to a patch of 6.1 Also 7.0 is scheduled to release in June, a patch would not appear a lot sooner anyway.
So you can open up a new case and ask about a patch, or you need to create a new file to checkin....