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We have two instances of a pallet with different runtime configurations. How can we run the benchmarks separately to generate two distinct sets of weights?

As far as I can tell this is not possible and if you list multiple pallet instances (such as in the kusama runtime here) it will use the last instance.

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It is possible. You just run the benchmark like for any other pallet.
The output will list the calls multiple times and finally print:

Created file: "runtime/kusama/src/weights/pallet_referenda_fellowship_referenda.rs"
Created file: "runtime/kusama/src/weights/pallet_referenda_referenda.rs"

Be sure to specify a folder and not a file path for the --output like in Kusama.
Otherwise it will overwrite the same file and print this as last line:

Created file: "runtime/kusama/src/weights/pallet_referenda.rs"
Created file: "runtime/kusama/src/weights/pallet_referenda.rs"
Multiple benchmarks were written to the same file: "runtime/kusama/src/weights/pallet_referenda.rs".

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