The crash was because when deleting the fluid sim domain geometry manta_set_domain_from_mesh would set fds->global_size to [inf, inf, inf] because me->totvert was zero. This would cause an error to be thrown in python saying the NameError: name 'inf' is not defined. Did you mean: 'int'?
There were two possible solutions to fix this. In fluid_script.h I could add the line from numpy import inf to the manta_import string, which fixed the issue, but I wasn't sure if we wanted to include the numpy module as it wasn't there already. The other solution is the one that I went with, which just sets fds->global_size = [FLT_MAX, FLT_MAX, FLT_MAX] instead of [inf, inf, inf] in the case that me->totvert == 0