From my understanding, as long as the rubber is in good shape, you should be ok.
Mine was chalky too. What I did, was clean the heck out of it with simple green, to remove the chalkiness. I then put two coats of henry's solarflex 287. I've been very happy since doing this. The roof is a nice white color, also the solarflex stuff keeps the inside a lot more cooler now. I noticed a big temp difference. I bought the gallon bucket for around $60. I used maybe 1/4 of it. I plan on adding more coats as needed during my roof maintenance checks.
Also, you could use the 5K shop repair quote, which is ridiculous, as a bargaining tool to lower the price of the RV.