The charge pump not being stable can mean several things. If it's not where it should be (it won't be) the high side fets won't turn on all the way, causing loads of excess heat inside the chip. This also may never recover, depending on the duty cycle, and then that chip will burn up/let the smoke out.

Essentially, the charge pump capacitor has a set of circuitry that brings the low side of it low, lets it get 5 or 12v, then floats it up to the voltage rail, to turn on the fet hard. If it's only partially on, the fet has a resistance that is too high. (The high side of the capacitor usually has a diode to charge it)

Usually, not adhering to timing recommendations isn't going to damage a circuit. However, it introduces potentially undefined or unpredictable behavior. For example, if you are driving a pump with specific timing requirements to control precisely the amount of fluid passed and you skew the timing a bit. Most of the time it would probably be fine, but there would be the potential that it might pump too much or too little. For a low precision application like a sump that's ok, but for a high precision application like an medication pump it has the potential to kill someone.

At the end of the day, it depends on your tolerance for risk. Manufacturers generally certify their products for the timing on their datasheets. If you operate out of those specs, you are taking the responsibility of what happens.

Don't want to scare anyone off, but it all depends on what you're doing with it. In personal projects, yeah I'll do all kinds of squirrely out of spec shit, but I'd never do that at work cause of potential liability. It's up to you to determine if losing a couple steps on your watering pump will kill anybody or not! :D