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Try to follow these steps:

  1. Close the Wireshark
  2. Delete stored commands that you wish in the file ~/.config/wireshark/recent_common
  3. Open the Wireshark again, so the filter history will be according to the file you changed

Likely the Wireshark keep the filter commands in memory while running, so the program will rewrite the recent_common file when closed. Thus, this operation must to do while Wireshark is stopped.