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eu-elflint --gnu-ld complains about a prelinked ET_EXEC when it had .bss split into .dynbss+.bss, because .dynsym symbols for bss symbols all refer to one section. Symbols that are now in .dynbss should have their st_shndx fields set to the index of .dynbss. This does not affect the dynamic linker, but does leave the symbol table in a nonkosher state. The same applies to .symtab in unstripped binaries for prelink, I expect. Similarly, the STT_SECTION symbols for allocated sections that were moved around by prelink should have their st_value's updated. Some linkers have produced section symbols even in .dynsym, so best to be thorough (or else edit the STT_SECTION and any other unreferenced local symbols out entirely if you are doing that sort of thing in prelink). It's possible that some debugger consumer would like to use st_shndx and can be confused by wrong indices, though most likely it's only elflint that cares.
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In the source it looks like this was fixed a while ago.