Disclaimer: IANAL; Best answer would be from a local lawyer with expertise in computer copyrights and laws at the location the owning company is at. If you'll be sued, it'll probably be in a court of their choosing as this is often part of the EULA.
However, one distinction I see here is that you don't modify the executable provided as part of the game, you only create a tool that does that. The actual person changing the game is the user of your tool. Abnother consideration though, is that most EULAs forbid reverse engineering, and you might be violating that.
Anyway, this is how I see you approaching this concern:
Approaching the rights owner
A way to get an answer for this is by approaching the company (or whoever currently owns rights for the game) and request permission / announce you're about to do that.
Consequences may vary:
Some right owners publicly waive some copyright protections of abandoned games, for the enjoyment and modification by the community. If that's the case, you'll be referred to the waiver.
If you're given permission, all is well and you're good to go.
If you're being ignored for a decent amount of time (say, a month) and later sued, you can argue the company had prior knowledge and choose not to forbid these actions in a timely manner.
If you receive an unofficial reply declining granting you the permissions (or the more formal Cease and Desist letter), at least you know where you're at.
Hoping for the best
If you choose not to approach the rights owner, you can infer potential reactions from past experiences (mostly of other's). Abandonware is indeed something quite common, and you can find games that are as far as fully emulated in web browsers. Investigating what other potential violations the same rights owner had in the past, and how it reacted. Finding other violations of the same game will also be good indicators.