Channelfly uses all 11 available 2.4G channels, while Background Scanning uses only channels 1/6/11, and should provide ~33% better client throughput.
Using the 'set channelfly wlanX mtbc 200' (mean time between changes) will decrease the frequency that you see APs change channels to avoid interference.
Only if you have clients which don't change channels well (Sky Box?) or VoIP badges, would we recommend turning off Channelfly, or better yet, run CF for a period of hours with default settings, then freeze your APs to those current channels when you disable it.
Client Load Balancing, which tries to equalize the number of clients on the same band of adjacent APs, will never disconnect already connected clients. It will withhold probe responses and association responses from new clients, if the AP already has 20 or more clients connected. Note: Client Load Balancing does not function if less than 20 (default) clients connected to AP radio.