Just as said in summary. For example, look at bug #468292. It seems that function need some additional checks for file type(probably some kind of MIME check? dunno).
Those files are autogenerated and therefore have quite a pre-defined format. I think we could try matching them by 'shouldnotlink=' line (which the function uses anyway).
Created attachment 347274 [details, diff] Suggested patch I'll submit it to the ml after testing.
+ 15 May 2013; Michał Górny <mgorny@gentoo.org> eutils.eclass: + prune_libtool_files: do not remove .la files which are not libtool files. + Fixes bug #468380.