Encouraging inventiveness is easy. You've already done it, in fact: You simply have to reward it by allowing it to (occasionally) succeed.
Avoiding breaking the game is also easy: You simply disallow anything that lets players to bypass the obstacles presented by the game with less effort than it would take to tackle those obstacles in a more traditional way.
Obviously, these two goals are hard to reconcile, but I can suggest a few things that might help.
First, let your players have the benefit of their invention, but remember to account for the costs: In your example, your alchemist has developed a devastating weapon, but one which eats through very expensive ammunition at a disturbingly rapid rate. Once the disparity between party member wealth levels grows a bit, he might start to worry. Also, given that it is a devastating weapon, even if it is expensive, ask yourself why other people don't use it. I imagine it would take just one orc with the Improved Sunder feat to make your player realise that there are pitfalls involved in waving acid vials over his own head.
Second, remember to include at least a few situations in which the invention does not work, to keep your players on their toes (and encourage future inventions): There's no end of creatures immune to acid and fire, so let them crop up occasionally - and your alchemist would be in strife if away from civilisation for an extended period.
Finally, don't be afraid to condtradict previous rulings if you can come up with a good reason for it. Yes, you should avoid it most of the time, but inventions are a special case, since by definition they're trying something new and unknown: Invention is inextricably paired with discovery. Be tactful, and start by saying "There's something I didn't think of that's kind of relevant to that idea you came up with," but be firm, and try and provide a reasonable in-game justification for it. "Your acid net? The ropes that make it up only have about two hit points, so it should be disintegrating every time you use it. Also, how have you been protecting yourself from the splash?"
Ask more generally about their comfort boundaries
Tell the party that you have some ideas you think might be crossing the line, and ask them where they'd like the line to be drawn. In that context you might even give examples and include something similar to your idea as just one of several.
Throw in a scaled-down version as a test
Use the general concept that you're concerned about as the inspiration for a minor encounter/adventure, scaled down and probably depersonalized (NPCs being the targets rather than the PC in question). Then watch their reactions.
This can have the added narrative benefit of foreshadowing and parallelism if you do go on with the main idea.
Ask a mutual friend
Present the scenario to someone who knows the player in question well but isn't involved in the game, and ask them for their opinion.
This is not an excellent option: the friend's guess might be wrong, and it's sneaky, so might not be appropriate for your group's trust dynamic.
Don't underestimate your players
I'm often surprised by how much better our games are when the players are clued in to what their characters have no idea about. It gives the players opportunities to consciously up the stakes and place their PCs in dramatically tense situations.
I liken it to the film style where the audience is shown something dangerous before the heroes know it exists, to increase the narrative tension without giving the heroes a chance to prepare for the danger.
Remember that effect of seeing your players pleasantly surprised by your plot twist only happens once, but building the story from that twist onwards is a combined effort. Sharing them in your plans lets them participate in building the story in a more proactive, rather than just reactive fashion. -lisardggY, in the comments below
Best Answer
I make sure to download or print a copy of the relevant errata so that I have it on hand when gaming. Then in the original source I will draw a small line (generally in pen) next to the text that has changed or received updates. Whenever I reference the rules and see one of those marks, I know to also reference the errata documents.
If multiple versions or additional errata are released, I will use a different color pen to indicate the source of the change. That makes it easy to know where I need to look.
I like this approach for several reasons:
I've been using this system for a number of years now and it's worked really well for me. One downside is that the information isn't immediately clear to another reader if someone is using my books instead of theirs to look up information. I see that as a very acceptable downside as it doesn't happen often.
I've also been considering writing page numbers in the same color next to these marks. I've not tried that yet, but I have noticed it can take a minute to find the right section if the errata document is longer than a page or two.