Because Solr's java modules use the com.xpn.XWiki.getSpaces and com.xpn.XWiki.getSpaceDocsName methods, when (re)indexing with Solr, you can either index all the documents or only not-hidden documents, based on the preference of the admin that performs the index operation. This is caused by the 2 methods that impose the hidden document filter on the internal query that they perform. This has been introduced by the "hidden documents" feature.
1. As admin, set your "Display hidden documents" to "Yes"
2. Go to the Solr Search Admin section in administration and re-index the wiki.
3. Now you should have indexed all the documents, instead of just the non-hidden ones.