After changing my engine to biber from bibtex to ensure my bibliography worked, it no longer recognises my cross-references to labelled equations and theorems in my script. They are labelled and referenced as follows:
...\label{equation}...
...\ref{equation}...
When I typeset in LaTeX the console reads as:
...LaTeX Warning: Reference 'FactCor' on Page 28 undefined on input line 748...
...Package inputenc Error: Unicode char \u8:ᅵ not set up for use with LaTeX

Package asthma Warning: Unknown theoremstyle 'theorem' on input line 34However this worked before. Also the error:Package biblatex Warning: 'babel/polyglossia' detected but 'csquotes' missing.– CS1994 Feb 02 '17 at 19:09\usepackage{csquotes}for the latter – idkfa Feb 02 '17 at 19:16\usepackage[utf8]{inputenc}into your preamble, delete all files created during compile (aux, bbl, ...) and compile again. If I take your code from this http://tex.stackexchange.com/questions/351775/how-to-successfully-put-a-bibliography-in-a-report-on-texshop question, that worked for me ... Does that work? Since I'm not sure how you're defining/calling your equations, I cannot test further. – Wiebke Feb 02 '17 at 19:49