In the real world, there are a number of common factors that can cause perturbations at check-in counters, such as an airport closure, a temporary power failure, crashing of the counter computer, baggage conveyor belt malfunctions, and so on, forcing the airport authority to reassign flights to new check-in counters. In this study, we develop a model and a solution method to solve common-use check-in counter reassignment problems with a variable number of service lines and a variable length of time window. To test how well the proposed model and the solution method can be applied to the real world, we perform numerical tests based on a hypothetical incident in relation to a Taiwan airport's operations. The test results show that the model and solution would be useful for the airport authority in actual operations.