The "Force Re-check" command appears to put the torrents it's checking into the same queue as the downloading/uploading torrents and gives them higher priority than the downloading torrents. This interrupts (pauses) any active torrents, which seems invasive and pointless to me.
Checking a paused torrent should not interrupt the downloading/uploading and queued torrents--as long as the files you're checking are saved on your local hard drives, which is the case for most users.