This is very dependant upon the correct and logical formatting of the input. It could probably be simplified through refactoring and needs a lot of testing, but the principles it uses might help:

##! perl -slw
use strict;

while( <DATA> ) {
    chomp;
    print, next unless m[TIMINGCHECK];
    my $count = tr[(][(] - tr[)][)];
    {
        s[^][//];
        print;
        last unless defined( $_ = <DATA> );
        chomp;
        $count += tr[(][(] - tr[)][)];
        redo unless $count < 0;
    }
    print;
}



__DATA__
...
(CELL
  ...
  (TIMINGCHECK
    ....
    ....
  )
)
(CELL
 (CELLTYPE "SEDFQD1")
 (INSTANCE uTrigger/TrcInclCtrlReg_reg[13])
 (DELAY
 (ABSOLUTE
  (IOPATH CP Q (0.10:0.15:0.25)(0.09:0.15:0.24))
 )
 )
 (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]

Output:

c:\test>junk6
...
(CELL
  ...
//  (TIMINGCHECK
//    ....
//    ....
//  )
)
(CELL
 (CELLTYPE "SEDFQD1")
 (INSTANCE uTrigger/TrcInclCtrlReg_reg[13])
 (DELAY
 (ABSOLUTE
  (IOPATH CP Q (0.10:0.15:0.25)(0.09:0.15:0.24))
 )
 )
// (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]