I agree with DR, after acetonitrile and/or buffer mobile phase/s have been used for a project, it is useful to flush the system with 85% water / 15%methanol. When buffers with a very high salt content are used, it is also useful to back-flush the pump pistons, please see the pump’s user manual.
Definitely a flush with buffer free mobile phase after. Another thing I have done, especially if the instrument will be used within a day or two after is to keep a very slow flow through the instrument of 50/50 water/methanol, about 0.2ml/min for non uplc systems. This seems to keep the check valves clean and also keeps the piston seals from sticking to the piston, which will cause wear on both once flow resumes. The pressure is normally low enough that it doesn't cause excessive wear on the pump seals and you don't worry about any microbial growth in the system.