Let's see what kind of passives you'd need to filter something to 10ppm stability in 1 hour.
Suppose the output is noisy, on the order of 1% (10,000 ppm) variation (it might be worse than this, but we can simply adjust everything by the same factor). You need 0.001% (10 ppm).
1 hour is a frequency around 0.28mHz (milli, not Mega). For a factor of 1000 reduction (that's 60dB) of AC amplitude, we need a cutoff frequency about (1000)^(1/2) times below that, for a 2nd order LC filter, or 8.6uHz.
The nominal output voltage and current are 10kV and 0.3mA, so the filter's characteristic impedance should be on the order of Zo = 10kV/0.3mA or 33Mohms. We might require that the amount of ripple the filter itself produces, due to varying load current, also be low; if it should be on the order of 10ppm, then we reduce Zo to 10ppm, or 330 ohms.
(Anyone familiar with filter design, should be begging to stop right now. I shall persevere regardless...)
The cutoff frequency of the filter happens to be the frequency where the L/C reactances are equal to Zo, so we can calculate them easily:
L = (330 ohm) / (2*pi*(8.6uHz)) = 6.1MH
C = 1 / (2*pi*(330 ohm)*(8.6uHz)) = 56F
This filter will be poorly damped (assuming neither the source nor load has a lossy impedance around 330 ohms, and the inductor's DCR is much less than 330 ohms, which it will need to be in order to satisfy the ppm requirement at DC as well), so we should divide the capacitor about in half, and add ~330 ohms ESR to one half.
The supply may have a constant-current characteristic, in which case we should put a capacitor on that side, too. We can save a bit on the total filter size, in that case, because a CLC filter is three poles, and only needs to be at about 1/10th the cutoff frequency. (Both capacitors can be split with added ESR as suggested, or ESR added to just one, accepting the modest degradation in performance.)
So, 10kV 56F capacitors, right? Yeah, so there's probably a lesson in there...
(It'll also take about a year of continuous on-time before it stabilizes within the desired margin, too!)
You can throw stupid numbers at a filter design method, and get proportionally stupid responses from it! GIGO. You need to reality-check your inputs in the first place.
So, this is why you can't simply filter the thing. The required cutoff frequency is absurdly low. For time constants in the ~kHz, filtering is relatively trivial -- a series resistor and a pair of modest value (~nF) capacitors will do an excellent job! For time constants in the ~Hz, you could maybe get away with some bigger parts, but, you'll be taking a long time charging them from the poor little power supply, and you'll be storing quite a lot of energy, which is expensive and much more hazardous.
For any longer time constant, you need a regulated control method. And for 10ppm, you need a high gain error amplifier, with low offset and drift. The amplifier itself will be operating at a couple of volts, so you need a precision (again, ~10ppm drift) resistor divider to sense the high voltage. That puts the amp at a 1000:1 (or worse) disadvantage, so it needs to be good to microvolts. Precision and high gain! It doesn't need to be very fast, so a standard (~one buck) chopper amp will do the job.
The error amplifier output drives something that controls the high voltage power supply. It might be a control input, it might be a pass transistor controlling the supply voltage, it might be a PWM modulator in a switching circuit, whatever.
And, that's basically it. I don't know anything about those "400kV" modules, but I doubt they're all that consistent (or quiet, in the Hz range where filtering is difficult!), and you need some way to control them (maybe by varying the supply voltage). You might be better off with a ZVS resonant or "chopper" oscillator on a flyback transformer, varying the supply to that. You can at least do it for a modest price, but measuring and verifying that it's actually working correctly will cost you a lot in test equipment, if you don't have it already!
Which leads to the most salient question: how do you even know when it's out by 10ppm, and either 1. can it be used for verification (repeatably), or 2. can it be made tolerant of such changes, so that an expensive power supply design is not required?
Tim