Noob Question: Replacing

[Diaz Ex Machina]

So I've found out that if I replace something in my source file with anything else the replaced thing won't show up anymore on HL even if my source isn't active. That's a bit of a bummer, because I'm using said source just for a single campaign, and all my other characters now are "flawed" to the core. What are my alternatives to replacing those items?

Just some examples of what I've replaced:

• All the core races (just needed to change the description and some height/weight values);
• All the items under Special Substances and Items in the Core Rulebook (wanted to give them new descriptions and change their order in the menu);
• All the Point Buy creation methods (altered their values and names);
• All the prestige classes from the Core Rulebook (tweaked a couple of them and changed their descriptions).

I've also precluded hundreds of things, but those appear correctly even with my source installed.

Thank you in advance for your help and time.