Unfortunately, Inkscape damages EPS files: it changes the colors and does not save all the objects. Over last years I tried to search for a solution, but I cannot find that people complained. The complaints (found on the Web) are related to something like "incorrect font rendering" when exporting from svg to eps or back. (For me this is not a problem - the text always can be represented as curves).
I currently work in Mandriva Linux 2010 and use Inkscape version 0.47 r22583 (Jan 14 2010). Somewhere I read that such problems could be caused by some outdated versions of cairo - mine is 1.9.14. I spend a lot of effort to build newer cairo (1.12.14), but I am still far from the purpose. I got confused in 32 and 64-bit libraries coexisting in my system...
I would be very grateful to anyone who has similar problems and, may be, advanced further towards the solution. Let me illustrate the problem.
(1) Here are the three eps images I would like to combine in one figure:
(2) Here is what I get after importing the images in Inkscape and saving in SVG format. Note color and resolution distortion. Also, I draw three red circles around the feature of interest.
(3) Here is what I get when I export this figure to EPS file. One can notice that one of the three red circles gone: only two circles left!