If you then use the "PS2 reset" batch this will cause the running application to be terminated, the IOP processor to be reset and reloaded, with PS2Link returning to the same initial state it had when first launched.
In the PS2PSXe context this means that you are ready for testing another game, without having to reboot the console in between.
Much of my own testing has been done using these batches, first drag-dropping game_1 onto 'run_PS1_CD' and then after some testing D-clicking 'PS2 reset', after which I drag-drop game_2 onto 'run_PS1_CD' to test that game, and so on with game after game...
But for testing of critical bugs I naturally always start 'clean' with fresh boot, to ensure that older tests (with potential remnant IOP effects) never influence the testing of such bugs.
Best regards: dlanor