I've had success using \import{subdir/}{BasenameInSubdir} from the import package.
The basic (and unfortunate in a xkcd/1479 way) issue appears to be that the arXiv compile server doesn't allow writing to subdirectories. A subdir \include implicitly requires write access for the aux file.
The basic (and unfortunate in a xkcd/1479 way) issue appears to be that the arXiv compile server doesn't allow writing to subdirectories. A subdir \include implicitly requires write access for the aux file.