Yes - those issues need to be considered
Even if you have a lift and a smaller implant, the skin that remains after your lift will be thin, stretched, damaged, and prone to stretching again.
You are correct that the blood flow to your nipple is already severely compromised.
Your situation in fact is more akin in its complexity to a post-mastectomy reconstruction case, though in a sense even worse because of the stretch of your skin.
My point isn't to depress you, but rather to emphasize to you that if your surgeon suggests a conservative, staged approach to your surgery, heed his or her advice. I often see patients choose the doctor who tells them what they want to hear. The complexity of your case is such that you should choose the doctor who demonstrates the most understanding and experience with your difficult situation.
Your case could be difficult
Thin tissue stretched by really large implants can make a difficult case for a breast lift and implant exchange particularly if you smoke. I would need to see you to tell you much more. You may need to be concerned about blood flow and tissue healing issues depending upon the way things are right now.
Implant exchange and lift
With 1000 cc's I assume you have saline implants. If you did not have a lot of tissue to begin with, you probably have thin coverage. Without examining you it would be difficult to assess what you specifically would need in terms of a lift.
You do not give your height and weight, but 1000cc implants do take a severe toll on your tissues(you already know this). Now if you have saline implants, what I would suggest is have your surgeon stick it with a 16G needle and remove about 200cc. This can be done in the office. Over time the saline will come out of the implant and your body absorbs it, but the important thing is that it allows your tissues to slowly relax and retract. This might take 2-3 months. At that time you can have an implant relacement and lift which is much less risky for tissue loss, i.e. nipple/ areaola complex. I've done this in a few patients that came to me with this problem and were grateful that I saved them an operation. If you have gel implants, obviously this plan will not work. You will need a staged operation.
In cases of extremely large pockets, synmastia, or the need for simultaneous breast implants and aggressive lifts, patients should consider staged surgeries. That means remove the large implant, allow a period of time to pass, then place new implants and do a lift. This will allow the skin to recover and the blood supply to reestablish itself.
It is tempting to "go" with the doctor who does a single staged procedure, but the complication rates for the very compromised tissues are very high. If a nipple dies and falls off (yes that is a real risk), it will never be the same even after a reconstruction.
One quick but not necessarily the best solution is to change the implants from below the muscle to above the muscle; however, this forever divides the blood supply to the nipple, especially an issue with revision or complex surgeries such as yours.
Most doctors would consider 1000 cc implants excessive, as you yourself can now attest.
Choose a breast implant that fits your breast anatomy and skin type
Your situation is complicated and more facts about your previous surgery/surgeries need to be known before any advice given, I think.
There are some general options although you have to decide how to approach your breasts aesthetically and safety-wise and what balance to strike between the two.
It is possible that if your skin is very thin, even a D or DD size would require an implant that will cause problems down the road. The prudent thing would be choose an implant that fits your breast anatomy. So the options would be to remove the implant and do a breast lift with the tissues you have.
Once the shape of the breast is optimized, this will determine the appropriate dimension of an implant that will "fit". The other approach would be to exchange the implant for a smaller implant to give you the size you want, then do a lift over this implant to achieve an optimal form.
As far as the nipple is concerned, tattooing the areola as in reconstructive case is a viable option to give it color and to camouflage scars.
You should have revision breast surgery in two stages.
In Manhattan, we almost always do combination breast lift and revision breast augmentation in one stage. But you are the exception. Without seeing you, it sounds difficult to get a good result safely.
So I would do it in two stages. First the implants should be removed, and a good mastopexy (lift) done. The lift has to be done INTERNALLY, without relying on pulling the skin. Otherwise, you get recurrent sagging, because the skin stretches. The scars usually fade nicely, specially around the nipple, even if the nipple is very pale.
Several months later, you can have reasonable size implants put in. I recommend using disposable implant SIZERS during surgery, to see which is the best size for you. This is done before the permanent implants are opened, and it takes the guess work out.
And go to another surgeon.. Anybody who put in 1000 cc implants does not have good judgement.