A good point; you don't have to start over from the beginning of your model building. What's most important is that the number and ordering of atom types in the PSF does not change. Reading the old PSF and deleting the water segment alone won't work if additional segments were added after the water, such as ions. In that case, you'd need to also delete the segments that follow the water segment in the PSF, and then add them back via GENERATE, in the same order as was done initially.