I have had several A/C companies give me bids on my air conditioning replacements. Most all have said the when changing the systems, that the R22 lines have to be replaced to carry the newer R40 freon. Last company said the lines only need to be flushed properly, and the can still be used. I am confused, to they older lines need to replace for the newer systems?

Depends, if you can not get them out, i.e. if they are in a closed space or celing then flushing is fine as long as the line size is correct. Flush costs almost as much as a new lineset so inless they are hard to remove them I would change them

They can be flushed BUT why bother. The cost of the proper flush material along with the labor is not cheap and then you have to find someone who really knows what they are doing. Also many times the suction line size needs to be larger anyway so that will have to be replaced if the manufactures install instructions say so.

Replace the lines and be done with it. This way you will have a complete new system.