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If we profile the slow version, we see that it spends quite some overhead in setting up a fresh state.
The effect of "reset" is to clear all state that was associated with the previous commands.
There is also different behavior with respect to pre-processing. check-sat from scratch uses a richer set of pre-processing simplifications that can have their own overhead. This is not directly visible in the stack below, but may in general play a role (some of the queries do take notable time, for reasons that are not visible from the global analysis).

Function Name Total CPU [unit, %] Self CPU [unit, %] Module
| - main 208648 (99.97%) 0 (0.00%) z3
| - read_smtlib2_commands 208648 (99.97%)

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@dong-yf
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@NikolajBjorner
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Answer selected by sreeshmaheshwar
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