I have some custom registers that I use to index some information. When 
compiled, it just prints [entry not flushed] instead of printing some of the 
page numbers.
I have tens of thousands of lines of code, so have no idea how to break the 
problem down to a minimal example. What does [entry not flushed] mean? What 
kind of feature in my document do I need to search for that might explain why 
this is appearing?

Here is the minimal code used in my index, as you see it isn't showing the 
error, so something else in the document is causing it:

 \setvalue{W3}{this is text for W3}


\defineregister[learnedshort][compress=yes]
\setupregister[learnedshort][style=sansbold, textstyle=slanted, n=3, 
pagenumber=yes, indicator=no]
%
\defineregister[learnedlong][compress=yes]
\setupregister[learnedlong][style=sansbold, textstyle=slanted, n=2, 
pagenumber=yes, indicator=no]
%
\define[1]\learnedis{%
    \txt{} \getvalue{#1}
    \learnedshort{#1}
    \learnedlong{#1}
}
\define[1]\learned{%
    \textreference[textref#1]{\expanded{\currentstructuretitle}}
    \reference[ref#1]{}%
%
    \learnedshort{#1}
    \learnedlong{\getvalue{#1}}
}

\starttext

\learned{W3}

        \startchapter[title=Standards]
              \placeregister[learnedlong]
        \stopchapter
\stoptext


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