You are getting good advice from doulos2k and -Istaril.
The word "instances" is, indeed, the relevant word in determining the difference between "lose all keywords" and "lose all instances of that/those keywords." The comment about "99.999%" is more about how uncommon (as in, "never") it is to see the term "all instances" in card text.
You should also note that the question answered by your quoted comment was effectively "if a character has stealth printed, gains stealth from a card effect, then loses 'all keywords,' will it be able to bypass something or not?" The answer was "1 (printed) + 1 (gained) - 1 (lost) = 1; so yes, the card can bypass something."
That answer leads you to what -Istaril is telling you: the order that modifiers are applied almost never matters. You always "start from scratch" when determining the result. So yes, things count less than zero all the time in this game when determining a card's status or characteristics. It's just that most of those characteristics interact in a "have or have not" kind of way. Having stealth twice, for example, doesn't let you bypass two characters because that's not how stealth works. Similarly, having -1 stealth doesn't make a character "more obvious."