You need to be careful as to why you needed to alter the length of one chain and not the other.
Chains wear, and get longer as they do so. A chain that has extended its length by more than 1% (so thats one Link in a 100 link chain) is due for replacement, not removal of a link.
Another factor affecting the looseness of chains is wear on the sprockets, and if one chain is looser than the other but they appear to be of the same length then it is worth looking at the sprockets.
Technically having one chain longer than the other shouldn't affect performance, but I cannot see how you could get that much difference with everything set up properly without having some serious wear going on.
(unless you have a chain tensioner in the system that is)
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