Auto body repair & detailing: Painting Base/Clear over body work, wet sand, bare metal

Question
I am restoring a 69 Charger and finished all body work (or so I thought) and painted base/clear on it about a week ago over 2k urethane primer. I've had numerous problems with the clear coat-dry spray, dirt in clear, etc. I ironed those problems out, but now I noticed some dents on the cowl yesterday and a low spot on the outside sail panel where it meets the quarter.   I sanded down through the clear to the base and covered them with putty. I have to repaint this area, but don't have enough in my pot to do this. I will need to buy another gallon of base. And if the shade is off, I will have to put a couple coats of base over the whole car again!
Can I: spray primer over the putty, wet sand it, shoot the base color on the area to build it up somewhat, then shoot the whole car in base, then clear?
Will it peel? Would I see it right away, or could it peel down the road?

Or, should I sand everything back down to primer and start over---My biggest fear is that if I just spot paint the puttied areas, the paint will peel. This will be the 3rd attempt at painting this car. After all the time and money spent on another gallon of paint, I DON'T want it to peel.
I asked the local paint shop and they told me I don't need to use primer unless I sanded through to bare metal. But also said if the color is off, I might as well sand the whole car back to primer and shoot new base/clear on it.
People I've talked to said that you can't paint over clear if you break through to the base color. I don't understand why. Do you have any advice on what to do?
Thank you!

Answer
Hello Dan
What color is the base? If it isn't a three stage pearl then you can blend it. The spots that you have had to repair should be blocked and primed. Now, block the primer and re-base the areas. If you have nibs of dirt in the adjacent clear, wet sand them. My suggestion is wet sand the car, re-base the areas you are concerned with , blend the color, and re-clear. When you reapply the base you need to be careful not to be to wet with the base or the clear will lift, if it does lift ,relax, just wait , sand the 'funny looking' areas and continue until you have the repair covered. Let me know how it works out.
You should not have to buy a gallon, a pint sounds like it would be plenty.
Dan