Tips:
- When making big changes, expect a whole lot of shit to get fucked up. Reason: Altium generates net names from random components on the net. Rename the parts (or pins!) and nets change.
- Usually, those changes are fine; whether they get resolved by brute force (old nets deleted, new nets added) or by matching (usually a tedious, manual process), they get resolved and you're fine. Sometimes the updating takes a while, yes.
- Prevent automatic net renaming by using manually named nets. These can also be descriptive (i.e., V_SW vs. NetC1_1), which gives you a potential reminder of what that net is, while routing.
- Occasionally, things will get really badly out of sync, and you kind of need to wipe everything. D, N, N (Design / Netlist / Edit Nets), select all (you have to select all in the list, CTRL+A doesn't do it..), delete. Import changes and they should all be back, and correct.
- If copper is getting out of sync, you can use D, N, U (Design / Netlist / Update Free Primitives..) to clean it up. Disclaimer: it doesn't always work the way you might expect, especially if you still have traces and stuff overlapping pads that changed nets!
Altium does things kind of odd, in that copper primitives have a Net property. Some EDA packages do that, some don't (e.g., Ultiboard always determines connectivity from pads alone). You can also correct it manually with S, P or S, C or S, S (Select / Connected Copper, Copper Single Layer or Physical Connection) and entering the new net in PCB Inspector.
Tim