If the plugin has the option
save minimal undo states enabled and it is removed
(either by alt-clicking the FX button or simply removing FX from right-click menu in FX chain), undoing that change doesn't always restore full plugin state.
This is really obvious with NI Kontakt. Simply load Kontakt, put some instrument in it and remove FX immediately by alt-clicking the FX button. Undo that change...Kontakt will get reloaded but there won't be any instruments loaded.
Definitely not nice since this can lead to data loss.
Would it be possible for REAPER to always save full plugin state when removing FX?
Vote here: http://forum.cockos.com/project.php?issueid=5576