When you call gst_bin_remove(), the element will be removed from the bin. Since the pipeline took ownership of the element (as it was a newly-created element, see “floating references”) when you added it, and the pipeline drops its reference when you remove it, that means the element will get freed, unless someone else still holds a ref to it. So you can prevent this by adding a gst_object_ref() before removing it.
You can track down these kind of issues (invalid memory access, use-after-free) with valgrind by the way. It will tell you where it got freed.
Having said that, I don’t understand this whole replace-filesink-with-fakesink thing while being paused. I don’t think it makes much sense.
What is the effect you want to have when pausing? If you playback the Matroska file later and you recorded for 10 seconds, paused for 10 seconds, and then recorded again for 10 seconds, how long should the playback be in your opinion? 30 secs or 20 secs? Should it show the paused part from 10-20 secs as ‘freeze frame’ or should it skip it entirely as if it never happened?
Perhaps you want a valve element in front of the encoder/muxer instead to drop data when you’re not recording? But if you want to skip the gaps you would also have to tweak the timestamps with gst_pad_set_offset() on the recording branch tee pad perhaps (and set an offset of -$time_paused whenever you resume recording) or somesuch.