This  document  lets  you  keep  track  track  of  your  chemical  structure  numbers  in  a  while  

LaTeX  document  down vote

You have two options:

1.- You can continue to use the packages {chemstyle} and {bpchem}but yes, you should add it as \usepackage[tracking=bpchem]{chemstyle} otherwise it won't keep track. if you do so, you then will have to define all structures embedded in the eps file as follows:

\begin{scheme}  %this  could  also  be  figure      \schemeref[TMP1]{XjU3o9}      \CNrefnolabel{XjU3o9}  %Note  that  this  **MUST**  be  identical  otherwise  the  numbers  will  be  different      \schemeref[TMP2]{A}      \CNrefnolabel{A}      \schemeref[TMP3]{B}      \CNrefnolabel{B}  ...so  on  and  so  forth,  depending  on  how  many  TMPX  you  have  in  your  scheme/figure      \includegraphics{EPSfile}      \caption{This  is  what  appears  in  the  bottom  of  the  scheme/figure  as  'title'}      \label{sch:Nameit!}  \end{scheme}  

2.- Don't use {bpchem} as your tracking package, instead use the newest version of {chemnum} (V 1.0). And actually if you don't want to have schemes in your document, you don't even have to use {chemstyle}! All you have to do is add \usepackage{chemnum} to your preamble and then you define your labels as follows:

\begin{scheme}  %in  this  case  you  MUST  have  the  `{chemstyle}`  package  loaded  in  your  preamble      \replacecmpd{XjU3o9}      \replacecmpd{A}      \replacecmpd{B}      ...so  on  and  so  forth,  depending  on  how  many  TMPX  you  have  in  your  scheme/figure  

   \includegraphics{EPSfile}      \caption{This  is  what  appears  in  the  bottom  of  the  scheme/figure  as  'title'}      \label{sch:Nameit!}  \end{scheme}  

NOTE that you don't have to include TMP1 or TMPX, the program will do it automatically, starting with TMP1, so be careful where you place those labels in your EPS file. As far as I am concern, you can also explicitly say which compound you want to be nicknamed A (i.e. TMP1 or TMP4) all you have to do is add [tag=youridentifier] between \replacecmpd and {nickname}. So for the previous example it'll be:

\begin{scheme}  %in  this  case  you  MUST  have  the  `{chemstyle}`  package  loaded  in  your  preamble      \replacecmpd[tag=TMP3]{XjU3o9}      \replacecmpd[tag=TMP1]{A}      \replacecmpd[tag=TMP2]{B}      ...so  on  and  so  forth,  depending  on  how  many  TMPX  you  have  in  your  scheme/figure      \includegraphics{EPSfile}      \caption{This  is  what  appears  in  the  bottom  of  the  scheme/figure  as  'title'}      \label{sch:Nameit!}  \end{scheme}  

And so TMP3 will be replaced by number 1, TMP1 by number 2 and TMP2 by number 3 once you typeset your document.

I hope this is useful for someone.

This answer was also published in http://tex.stackexchange.com/questions/51666/problems-with-numbering-compounds-using-bpchem/172526#172526 if you want further information.