When you save the project file again, it will tell you that it's saved previously in e.g. v5.1 and you're now in v5.6. You can then cancel it.
It's also in the xml in the project file itself, at the top.
<?xml version="1.0" encoding="utf-8"?>
<!--LLBLGen Pro v5.6 project file. Do not manually edit this file. Incorrect references could lead to an unloadable project file.-->
<Project Version="5.6" TargetFrameworkName="LLBLGen Pro Runtime Framework" UseLegacyDefaults="false">
...