Well... IANAL, but date/time stamps on files created on a specific machine get that information from the CMOS clock, which you can set to whatever time and date you want. So, you really can't say that the files with those dates that are on your computer prove anything. However, the files that are stored by someone else, if they have been stored by someone else for as long as you say, prove that they did indeed exist before you worked for this company.
So the project stored on GitHub which confirms the fact that the files are from that era isn't beside the point, it is going to "be" the point... or the lynchpin in this case. Whether or not a court accepts the validity of their information is going to decide on whether you created this software before you worked for this company.
The point might be moot, however. If you worked on the software on company time, you might still be contractually obligated to turn it over to them. It all depends on if anything you signed before you worked there says that anything you DEVELOP while working for the company is theirs... since DEVELOP doesn't necessarily mean create. It could be interpreted as improving, or working on.