There are no separate lines for check in. If you have luggage and need a physical check in you will be escorted to your Y/J/F check in line with the operating carrier where you will wait your turn. I haven't done it at CDG for departure so unclear if they queue jump, staff may call you forward.

For security and immigration you go bypass the queues entirely.

M&A is unaffected by the current issues, other than they may not accept your booking if at capacity.