Feel free to fill the upstairs cistern with a bucket and flush that way....although you can simply pour water down the pan from the bucket to achieve the same thing.
If your boiler is showing low pressure at the gauge, this is purely to do with the sealed central heating (radiator) system - and nothing to do with your problem here. However - if your boiler pressure falls to zero, a fail safe device could prevent it (the boiler) firing up. Aim for a pressure of between 1 to 2 bar on the gauge. More than 3 bar will cause the pressure relief valve on the boiler to open which can be a real bore.
You say that the downstairs pressure seems to be lower than normal now? Therefore I must conclude that for some reason, the mains water pressure to your house is lower than it should be. This could certainly prevent water flow to the upstairs, but your central heating - if you are using it - will be unaffected. I just can't think of anything else - and I do hope you find the problem! Best wishes!
John
August 2009