I have a 1/1000 chance of dying during this surgery

Do you have a source for that? Because after doing my research, what I've found is that a 0.001 mortality rate after gastric bypass seems to be a fair estimate. And while that is 1 in 1,000 patients dying, that doesn't necessarily mean you have a "1 in 1,000th chance" of dying. That's not how statistics and probability works.

That's like saying "Well if I have a 1% of having an item get dropped after killing a monster, then after 100 kills I am guaranteed to get it because that's 1% times 100 which = 100%"

There are more variables at play here like your weight, age, body fat%, diabetes, potential hypertension, etc which could put you at a higher risk than other patients. 1 in 1,000 patients dying isn't a percentage of survival, but even if it was, that would only be for an average patient. Like I just said, if you have variables that make you riskier or less than the average patient, your percentage of survival changes as well. That's statistics.