The BATFE requests notification of changes. It's not required. I wouldn't notify the BATFE personally, unless I was going to sell the upper that you have listed on the Form 1.
You can have multiple short uppers for 1 SBR lower. As long as all your uppers have a legal place to go, using all your lowers, you're good. They don't all have to be attached at the same time.
IE: you have 1 SBR lower. You have multiple short uppers. Each of those uppers can legally be attached to your SBR lower. Thus, they all can be used legally.
You may get into a grey area if you have non-sbr lowers and not enough >16" uppers to put on all your non-nfa lowers.
IE. You have 1 SBR lower and 4 Title I lowers. You only have 3 >16" uppes and 2 <16" lowers. You are in a grey area here. Yes, both <16" uppers can be used legally on your SBR lower but you now have an extra Title I lower and an extra <16" upper. If someone got a hard on about it, they could come to the conclusion that, that extra <16" is for that title I lower.
Make sense?
ETA: To answer you question. If you wish to notify the BATFE anyway, all you need to do is write a simple letter saying you are the registered owner of x item xxxx serno. You will be changing the length of the barrel to xx.x inches.
IIRC if you send two copies and you request so, they will stamp "received" and mail one back to you.