I was having this problem while trying to create reports - once they're finished they don't need to change, but while I'm making them, I keep adding new lines and each new line mucks up the conditional formatting.
This is by no means a good solution, but it was the best I could find without resorting to VBA - which was to:
a) Make the conditional formatting rules apply to a whole column or more at a time
for example instead of setting conditional formatting on C2 and C17, put an extra column, and write "this one" in rows 2 and 17, and then set the formatting for the whole of column C to be "if the other column says 'this one' then apply this format"
b) Change the Applies To to be just $C$1:$C$2.
c) Make changes and insert rows and stuff
d) Then go back and change the Applies To to be $C:$C
That way, while you change things and add things, the conditional formatting isn't there, but then you put it all back later.
If, at a later date, you need to add a few more rows, first change it from $C:$C to $C$1:$C$2, then make the changes, and then put it back to $C:$C. That way you don't have to completely rewrite all the formatting rules from scratch as you would if you do what I've done previously which was just delete them all, curse, and start again ;)
Obviously if you're planning on inserting rows up at the top in row 1 or 2, that won't work, but you could always set it to some other rows that you know you won't change.