I just went thru this with a Jeep we were working on. The lines if rusted, should be replaced. Regular brake fluid,(non-silicone), absorbs water, so if they are rusty or questionable, they should be replaced as they will cause a myriad of problems. If they are 'OK' then you could run some solvent,(Parts cleaning solvent) thru them but you have to make sure you can get all of it out. Silicone brake fluid doesnt absorb water but then the water that eventually gets in the system from condensation will sit at the lowest point in the system and cause corrosion. This would be a very bad thing if the lines are already compromised. Youve come this far,,dont 'shortcut it' if you can