I can confirm this with Mavericks. Sequential importing three files deletes all previous imported events. This must be a change to Calendar, because in the past it was possible to Merge iCal Calendars by importing multiple files.
Sorry, at the moment I have no workaround.
I must correct my last post, merging calendars by exporting and reimporting multiple files still works.
By my first Test i created a new Calendar with one Event and exported this to file one. Then I moved the Event to another day and exported this to file two and so on. By doing so, there is only one unique ID in all files. For testing, you must allways create a new Event to get unique IDs for the Events.
If merging by reimporting multiple ics-Files does not work for you, there must be a Problem with the stored UIDs. You can check this for some Events by opening the files with TextEdit and controlling the used "UID:".