Keeping track of definitions
Whenever I am doing a mathematics-heavy piece of writing (in LaTeX, of course), I tend to track the formal notation with two tools:


Every piece of notation (symbol or otherwise) gets its own \newcommand, which is used religiously.
At the first point where formal notation starts to be used, I add a table of notation that includes all of the significant notation.


It is further typically the case that each of these is broken out into its file (e.g., notation.tex, symboltable.tex) that is input into the main document, so that there is no chance for the definitions to spread around into different parts of the document.

There are several nice things about using this approach:


Using LaTeX commands for notation ensure that notation will be consistent
It is easy to change notation by changing the contents of the command
When you remove a piece of notation, you can delete the old command and be assured of errors anywhere that the command remains
The commands file can be used as a checklist for completeness of the table, and the table as a checklist for completeness of the definitions in the text body.


In many cases, the table may not survive all the way to submission (though I very much like to have one, it is an easy thing to cut from an over-length paper), but adding or removing it is just one \input line to comment in the source file, so it can still be very much a part of the manuscript development process, even if it's not showing up in the final manuscript.