Removing custom attributes is a little less work than adding them as you have seen. You don't have to explicitly run SyncUI when the attribute is removed, however if you have done any specific placing of the custom attributes on the AST forms, you may need to look at that to keep it neat.
Example, you add field CUSTOM1 to the ComputerSystem class, run SyncUI, then go to Dev Studio to locate the new attribute and move it onto a visible tab so it can be seen/used. When you remove it, it will be gone from the AST form, but there will usually be a gap where it used to be, so for cosmetic reasons you could run SyncUI again which will probably lay things out better again, or just use Dev Studio to tidy it up.
Edit: Actually just remembered that SyncUI, by design, will not alter changes you have made to AST forms. So those 'gaps' if they exists where deleted attributes used to be, will need to be cosmetically fixed in Dev Studio.
As Carey mentioned, there is no need to run SyncUI.
In fact there are two cases ONLY when you want to run SyncUI (I could not really think of other cases)... if someone knows correct me please.
1) You created a new class for which you want an AST form.
2) You created a new attribute and you want that attribute to reflect in the AST forms.