Not sure what was actually instructed when but not sure how why CE2 was instructed at the same time, unless it was a proposed instruction under 61.2. You don't know if you need to reline as it is dependant on the test.
CE1 should have been assessed as to how long it would take and how much it would cost as a forecast, and then if you were to assess CE2 it should have been the extra over effect CE2 would have had once the forecast cost of CE1 had been considered.
Why it took so long to get the pipe tested is not clear here and why it took three months. If the reason it was held up was for another reason that would be a new CE you may need to consider that. If you didn't need to kick your heels you shouldn't have. If you assessed the cost and time implications of lining the pipe and agreed them, and now the effects are worse that will be Contractor risk unless again there is a new CE you didn't know at the time of assessing CE2.
CE1 should have been assessed as to how long it would take and how much it would cost as a forecast, and then if you were to assess CE2 it should have been the extra over effect CE2 would have had once the forecast cost of CE1 had been considered.
Why it took so long to get the pipe tested is not clear here and why it took three months. If the reason it was held up was for another reason that would be a new CE you may need to consider that. If you didn't need to kick your heels you shouldn't have. If you assessed the cost and time implications of lining the pipe and agreed them, and now the effects are worse that will be Contractor risk unless again there is a new CE you didn't know at the time of assessing CE2.