Your captian has 1000 Fed points.
You drop faction and go do a KDF mission that gives you 10 KDF points.
Your captain would then have 990 Fed points. you would have to do this untill you reache 0 Fed points Then you could start making Kdf points.
so once you join a faction it would take double the points to switch sides.
The cost to join Feds is 1000
You drop the FED faction and make KDF points 1000 to remove the points you already have in your FED pool. Then you make 1000 KDF points for a total of 2000 to switch to KDF.
Now lets say you want to go back to the Fed side. The fed point requirement would raise to say 2000.
You would then have to negate your KDF points and then raise 2000 FED points to join back with the Feds.