It is explicitly summed up in Looper:
It's interesting to see that a file on Enchantress was included in Waller's metahuman dossiers, since the Squad defeated her. Enchantress' file was likely included for two reasons. First, the dossiers were on metahumans in general, so Waller's judgements on character weren't really a factor in assembling this information. Enchantress was featured so Batman could develop countermeasures in case the witch's spirit, or someone with powers similar to hers, were to ever go bad.
And also, it is noteworthy to quote the following excerpt from ComicBook.com:
[...] After his meeting with Waller we now know how Bruce got his leads on the various League members whereabouts, and that he knows information well beyond the existence of metahumans. With the intel about The Enchantress clearly visible in the file, Bruce now knows that the supernatural and mystical are also realities in this brave new metahuman world.
So, in a nutshell the reason was that Waller wanted to make Bruce aware of the threat of Enchantress in case she or sort of equivalent rises again.