Yes, you can flush a toilet while it is currently refilling or running, but doing so while the tank is nearly empty will result in a weak, ineffective flush because there is insufficient water volume in the tank to trigger the siphon action. It is mechanically harmless to the plumbing, but waiting until the fill valve completes its cycle ensures a full reservoir of water is available to clear waste properly. Verification: Check that the tank has finished filling completely before flushing to ensure maximum siphon force.
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