Hi Krishnaprasad,
From my testing, it seems that the issue is that Basilisk can only restore the simulation when the mesh has an exact power of 2 in each dimension i.e. 2, 4, 8, 16... cells in every dimension. Therefore, you can only restart if your aspect ratio is also a power of 2. The only "fix" in that case is to make your geometry a little bigger. In my case, I was trying to simulate a 40x1x1 channel and instead I simply extended it to a 64x1x1 channel. Depending on your problem, you may or may not be able to do this or may need to include an embedded boundary along with this fix to create your geometry.
Brandon Aranda