A channel (listed in Channel / EPG) should not just reappear unless you're using a bouquet, in which case this is correct behavior, you can however disable a channel and it should remain disabled unless the underlying service gets changed in some way, new pids, name change etc AIUI.
If you're using 4.1.x you can mass edit selected entries. Highlight the ones you want to disable (using shift/ctrl+click) and press the edit button - just click the checkbox before the setting to apply it to all selected.
HTH.