In my case I thought I got to 10000 flux (base capacity) by using the system - and ship overloads when it hits the cap, which is what happened.
That screenshot I got was the best thing I could get reliably - I don't exactly want to go frame-by-frame and find exact moment I use the system, hit 10000 flux by doing so and overload
I thought Phase Cloak overwrites the soft flux with hard flux? That's not a thing?
Only thing that gives soft flux to phase ship are its guns and the system as far as I am concerned.
The ship overloads when it exceeds the cap, not when it hits the cap. Phase cloak adds hard flux, which means that if say you have 1000 hard flux, and 2000 soft flux, and you add 100 hard flux to it, you'd have 1100 hard flux and 2100 soft flux.
Okay, bit of derp on my side about overloads
And now I'm confused about cloak.
Assume we're in phase ship, I have around half of my capacity in soft flux.
When I activate phase cloak I get hard flux equal to activation cost, then as I keep being phased, I get more hard flux (due to soft flux being overwritten by hard flux), but my overall flux keeps dropping due to soft flux being dissipated, as long as there's soft flux to dissipate.
That means I overloaded myself by going over the cap by using the system, which shouldn't really
happen?
And on screenshot I included (though it's not really that good, so it can be hard to see) - around 4/5th of capacity is hard flux, rest if soft flux, so...
I don't know anymore
It's not overwritten and Alex does a poor job of explaining.
Better to think of it like this, Soft and Hard flux are too separate things. You have 1000 soft and 1000 hard, equaling to 2000 total flux. You gain 100 hard flux because you used your phase cloak, but in that same time you lost 200 soft flux from dissipation, you now have 1100+800=2100 total flux. The soft flux was not "replaced", you simply lost some soft and gained some hard.
The way he describes it, Soft flux and total flux are interchangeable terms. It's easier to see the effect though if you consider them as 3 separate numbers. The way it works in game is the same.
As for why the overload happens, it's because dissipation and maintenance flux aren't exactly continuous, and they update at different times. Say you had 1499 total flux out of 2000 max flux. In one instant of game you gained 500 flux from using the ship system and 2 flux from maintenance. You would have then lost 3 flux from dissipation, but because that calculation hasn't happened yet, you are now at 2001 total flux out of 2000 max, meaning you overloaded.
It might be somewhat more intuitive to design the system to calculate maintenance minus dissipation together and only update total flux once instead of twice. That's the way it probably works in your head, but in the game it's different. But then, soft and hard flux totals still have to be adjusted separately each tick, so that probably just complicates things.