I am sure that the knowledgeable and very helpful Dana will reply shortly. In the meantime here is my experience, as someone who often struggles with printers.
Doing what you did is something that I'd only do very, very, very rarely and only to try to deal with an intransigent clog.
I'd only do it with carts removed, because the effect is likely to be what you experienced - something wet in contact with the print head will wick the ink away and drain the carts.
You can suffer the same fate if you over-fill the capping station with flush solution and don't gently towel it away before parking the head there.
The way you avoid running out of ink is to refill the cartridge and reset the chip at the same time. The Epson software doesn't measure what's actually in the cart - it only measures usage, and not even that - it only measures how often it tried to fire each nozzle.
The only way to be really sure how much is in the cart is to pull the cart out and look. For roughly 6 of the 8 carts you can do this with the printer off if you remove the lid that covers the carts. This avoids a head clean from removing and replacing the same cart. But it shouldn't be necessary if you don't create the conditions where a cart might drain.
The other way to avoid running out of ink - from a cartridge draining - is to follow the filling procedures exactly and perform the printer cleaning procedure occasionally.
I sympathise with your desire to avoid head cleans and the frustration that comes from getting gaps in nozzle checks too often. Printing a purge pattern can often clear gaps in nozzle checks at a much lower ink cost that a head clean. You can target just the blocked channel if you create a custom QTR curve that uses only that channel.