How do I reduce the lemon acidity in apple soup?
It may be worth trying to balance the sour flavor out using some sugar or other sweetener, it will be powerfully flavored but it's better than adding baking soda, as it has been pointed out that may change the texture and flavor in ways you do not want. At the very least it may reduce the amount of acidity you would want to neutralize, so less baking soda would be needed. 

As for what I'd do: chuck it and start over if adding sugar doesn't work. I wouldn't make another batch and combine the two because if you combine them and it still doesn't taste good you have wasted 2 batches! I'd start over and try to get the second batch right, then you have a better chance of getting something out of your efforts. 

How much lemon juice and/or rind you need to add is dependent on personal taste, the type of apples used and their acidity (there are apples that are too sour to begin with!), and other factors like how much water is added. A recipe in this case is a guideline, you should start with far less lemon and sugar than the recipe suggests and add more of both gradually, tasting as you go. If you use granny smith (very, very tart) apples you'll need much less lemon and much more sugar for example.