Are personal tools that were created by an employee of a company owned by the employee if they were not commissioned by the company he worked for?
The scenario is as follows:
Would it be possible to write a 2.0 version to sidestep legal issues?
It depends on the contract you signed when you worked there. It's typical for there to be a clause saying anything you write belongs to the company, especially if you wrote it on your work PC. You might be able to negotiate it if you left on good terms with the company.
You don't have any legal issue to sidestep. If they were written by an employee in the normal course of their job with you then they belong to your company. If the employee ever came back and claimed that you were using their software then the fact that they wrote the tools on your time, while being paid by you, and left them behind and you have been using them since, means that you have a de facto agreement to use them which is what any court would look at in the absence of a license.
I bet too that his employment contract stated that anything he did during his tenure with your company was owned by you, so you are covered in any case.
So you don't have to write a v2.0 to overcome any legal issues. You may have to write one because you don't have the source code, but that is quite a different matter.
As a matter of interest, where is the source code?
It depends on the laws in your country. I live in Germany, and here something developed during the course of your work is considered to be owned by your employer. It does not matter if you were given the task to do that, or did it out of your own initiative.
This gives the company the right to do everything they want with the tools, including deassembling or decompiling them.
By the way: IANAL.