I have just upgraded my site, which has a lot of texts that use footnotes. These were generated by a little module I wrote to overcome the problem of always getting switched into the home page when I clicked on the note reference (this used to happen in 4.6). Here is what a footnote reference looks like in my site:
<a href="ir/127/hungary-1956#_ftn6" name="_ftnref6">[6]</a>
and here is the link back up again
<a href="ir/127/hungary-1956#_ftnref6" name="_ftn6">[6]</a>
In order to convert my site without having to close down the live site while I upgraded in situ, I backed up the database, made a copy of the 4.6 installation in another directory (another URL therefore) logged in, replaced the 4.6 with the 4.7 version, and did the upgrade. When everything worked, I moved the 4.7 code into where the 4.6 code used to be, and there was my site back where it should be, but this time using 4.7.
Somewhere along the road, all my footnote references got converted so that now they look like this:
<a href="/470/ir/127/hungary-1956#_ftn1" name="_ftnref1">[1]</a>
and here is the switch back up
<a href="/470/ir/127/hungary-1956#_ftnref1" name="_ftn1">[1]</a>