Yes, this workflow is supported, but it has to be performed from the start, rather than after the fact. Here's what I mean by that.
The subfiles package provides the means to actually have individual sub files that are included in your main .tex file (using \include or \includeonly) but also are compilable themselves. The package should be included in the main .tex, while each subfile has a working preamble. You can then iterate (loop) over the respective subfiles (chapters in your case) using a standard bash script, and compile each chapter using latex, pdflatex or xelatex. For example, under DOS, the following should work:
for /f %%a IN ('dir /b Chapter_??.tex') do call pdflatex %%a
You may have to run this entire script at least two times for references in each chapter to work.
The standalone document class provides a similar functionality, skipping preambles of included files and only considering content contained within the document environment when compiling the main .tex. Included files, however are individually compilable.
The main drawback from compiling this way is referencing across chapters and page numbers that will restart at 1 for each chapter. The former might be addressed using the xr package, while the latter may be addessed by inserting the respective page number modification in the document preamble (via \setcounter{page}{...}), perhaps even reading it from the main .aux file. Regardless, this fiddling may be difficult to master if not set up properly.
hyperrefpackage, that is perhaps less work. – Torbjørn T. Oct 12 '11 at 14:41