Very new to all of this, but some of the values in the default properties really irk me, so I'm experimenting with 'improving' some properties. However, it seems that HDTP will only run if it has its own version of Deus Ex.u tucked away in the HDTP\System directory in its untouched state. If I do any change and then 'ucc make', HDTP is no longer present in the game.

Is there a way to keep the nicer textures of HDTP and tweak the .uc files via a newly compiled Deus Ex.u?

Well, you could, instead of rebuilding the default DeusEx.u, rebuilding the HDTP version. The Shifter (and other similar mods) also has HDTP functionality that is a little more flexible from what I can make out.

HDTP is a new version of deusex.u: the only way to implement mesh, texture and mesh/texture-related coding changes (like visible weaponmods) is to stick it all in the core code package. Obviously all the mesh/texture packages are necessary too, but they're useless without the code to implement them.

However, the actual recoding of deusex.u that HDTP uses is...mild, to say the least. Thus as long as you know what you've changed in deusex.u, it should be easy as pie to simply change the same variables in the HDTP version.