There were bugs in some toolchain tools, see bug #698005, that could cause a main ELF file the separate debuginfo file to have different header types/flags. eu-unstrip would not combine such files. The same was true when the main ELF file was prelinked after the debuginfo was separated into a debug file.
The ELF file and the separate debug file could not be recombined into one with eu-unstrip.
eu-unstrip now explains which header field doesn't match when it refuses to combine a stripped and unstripped file. e.g. "ELF header identification (e_ident) different."
And also now has a --force option that will warn, but try to combine such files anyway. That works fine for ELF files produced with the buggy binutils from bug #698005.
For prelinked stripped files it might work, but eu-unstrip also produces a warning if the DWARF data might need adjusting for prelinking bias (DWARF data in 'merged' not adjusted for prelinking bias; consider prelink -u).
Such mismatching main ELF and separate debug files can now be recombined into one using eu-unstrip, using the --force flag.