tl494 library altium
No, just like any other software - newer formats cannot be read by older software. DXP allows more layers, more design rules, more features, has different functions - that is why the files aren't backward compatible.
The only tool that allows DXP files to be converted to 99SE format is DXP itself. DXP allows you to save files in older formats - with the understanding that you will lose newer features and layers in the layout when you convert to the older formats which do not support them.
99SE is good design software, and will work well for your projects. If all you are going to do are simple two layer or four layer boards, then Protel 98 or 99SE ARE the right versions to use. AD2004 (DXP) is professional grade software, and will allow you to do many more things with design and layout. There are some drawbacks to using AD2004 for simple hobby projects. Because AD2004 is loaded with new capabilities, it takes longer to learn, and it demands more of your computer and video card.
If you plan to advance to AD2004 (DXP) eventually, whoever told you to start learning Protel with 99SE was giving you bad advice. DXP uses an entirely different file structure, different operating environment, different rule logic - aside from a few hotkeys that are the same, you'll have to learn to do things all over again when you start using DXP. You would have been better off to start with the better software, and that is AD2004 with service pack 4 (the most current version of DXP).