I would say aim to remove and replace no more than 1/2 the total volume of water at a time.
In my opinion, it is not only possible to remove too much water but also possible to remove too much debris from the gravel. If you are using this much water to siphon then I would guess that you are risking removing too much bacteria at once.
The balance that makes a planted tank work is partly due to the establishment of bacteria that exist partially in the filter, but also in the substrate and water column. You can take a well balanced planted aqarium and overclean it and observe problems developing shortly after.
I do not know if you are siphoning only the topmost layer of substrate or if you are deep cleaning your substrate. When deep cleaning, it is usually recommended to do so in 1/3 or 1/2 sections rather than deep cleaning the entire substrate at once. The reasoning is that there are beneficial bacteria living in the substrate and removing all of them at once denies them time to reestablish themselves in large enough numbers to continue to process your chemical waste without interruption. The interruption could manifest itself in an ammonia spike or other such symptoms of a sudden decrease in your biological filtration.
As far as the water being removed, this is an issue if your new water isn't exactly the same as your old water. Ph, chemical composition, Co2 levels, temperature...all these possible differences are negated or at least lessened if you leave a reasonable amount of your original water in the tank because it issentially "dillutes" the differences and reduces the shock of sudden changes.
IMO, it is not adviseable to routinely remove I would guess more than 75% of your water in a large established tank unless you are draining the tank or removing a serious contaminant or poison.
"Insanity: doing [or asking] the same thing over and over again and expecting different results."
Last edited by random_alias; 09-19-2005 at 08:46 AM.