Hmmm... have you ever heard about the concept of archive? It's a single file that you can copy around, but it contains literally several files inside!
Another option is to tell the operating system to deallocate part of the file, turning it into a sparse file. This can be done with fallocate(FALLOC_FL_PUNCH_HOLE) on Linux, FSCTL_SET_ZERO_DATA on Windows.
Linux also has fallocate(FALLOC_FL_COLLAPSE_SIZE) which lets you actually remove a byte range from the middle of a file, shifting up everything that comes after that byte range. So, in fact, you can "move" bytes in a file, on certain filesystems on Linux (ext4, xfs, among others).
Unfortunately, support for sparse files is quite variable across platforms. The macOS equivalent to fallocate(FALLOC_FL_PUNCH_HOLE) if fcntl(F_PUNCHHOLE), but the issue is HFS+ has never supported sparse files. UFS did, but UFS support was dropped from 10.7 onwards. The support is supposed to be back in APFS, but I don't know if it actually works.