Union members had been striking since BAE lost a High Court bid to prevent walkouts in November.
The Unite union accuses BAE of altering offers 'at the last minute' as staff return to strike action.
Lancashire is bidding for a share of the government's Local Innovation Partnership Fund.
About 100 union members have downed tools at BAE sites in Warton and Samlesbury, says Unite.
BAE Systems lost a High Court bid earlier this month to prevent workers from taking strike action.
Union members at Warton and Samlesbury had voted to strike after rejecting a 3.6% pay offer.
Workers at the Warton and Samlesbury sites are set to start industrial action from 5 to 25 November.
The Unite union says its members will walk off the job after rejecting a pay offer of 3.6%.
More than 5,000 workers based at BAE Systems in Warton and Samlesbury rejected the latest pay offer.
