Yes. Hence my "This is very dependant upon the correct and logical formatting of the input." caveat.

If there are any errors in the balancing of parens, it will fail horribly, but as the text is obviously source to some parser somewhere, it's a reasonable, pragmatic, economic ROI decision to say: This 'comment out timing checks script' is only usable on source that parses correctly using a.n.other tool. A pragmatic decision to save having to reverse engineer that a.n.other tool's parser from scratch and without the originial specs.

It will also fail in many cases that would (probably; no spec!) be successfully parsed by that other parser. For example, if the close parens placements are coalesed on a single line, rather than laid out in a logically structured way as per the OPs example:

(CELL
 (TIMINGCHECK
  (SETUP (posedge SI) (posedge CP) (0.14:0.23:0.41))
  (SETUP (negedge SI) (posedge CP) (0.09:0.16:0.30))
  ....(random lines)
  (HOLD (negedge SI) (posedge CP) (0.00:0.00:0.00))
  (HOLD (negedge D) (posedge CP) (0.00:0.00:0.00))
 ))
[download]

In this case, the close paren of the (CELL block will also be commented out and the result will fail to parse with that other tool.

In an ideal world one would go back to the authors of a.n.other tool, request a copy of their parser, or the specifications from which it was drawn, and produce a 'proper parser' script that understood all the rules of the input language and performed the required operation.

But this isn't an ideal world, and time is money, and performing ad-hoc text munging tasks like this are exactly what Perl was invented for. (Amongst other things. :)

But then again, it seems that the authors of a.n.other tool were either on-the-ball or responsive to in-use experience of using their tool, because it seems they already may have provided an option that make this entire thread redundant.

It's just a shame that post hasn't received the attention and votes it deserves. It's a non-perl solution, but, assuming the poster has correctly recognised the nature of the data and OP is using the correct a.n.other tool, by far the best solution to the OPs problem.