I would export the preference before modifying the color, and then after.
That way, you would be able to isolate the specific rules of an eclipse preference file into one smaller file and:
check if some colors not restored are indeed represented by a rule
the import of a smaller preference has any effect on the previously unchanged settings.
That kind of strategy can be further refined into several small settings files (one for Java, one for JSP, HTML, CSS, ...), in order to better analyzing the potential side-effects when re-importing those settings.
I just wanted to mention beforehand that I did try to start with a fresh Eclipse install, export the preferences to a .epf file, change just one single setting, export again, and compare the files. To my surprise, trying to import settings from a minimal .epf file did not work reliably either.
The solution that worked for me was to copy these files: {Eclipse workspace directory}/.metadata/.plugins/org.eclipse.core.runtime/.settings/*.prefs
I tried a fresh Eclipse install on another machine and after copying those files over, all my settings were restored perfectly.
I have deleted recently changed *.prefs file from the following dreictory \myworkspace.metadata.plugins\org.eclipse.core.runtime.settings\ and imported existing exported preference.
I am the first person, who answer for this question as per my knowledge :), Cause even I struggled lot.
The solution was to copy SOME - not all - of the files from {workspace}/.metadata/.plugins/org.eclipse.core.runtime/.settings/*.prefs into my other workspace.
If you want to be a little more fine grained on what you migrate, the syntax highlighting rules are the lines starting with semanticHighlighting on workspace-indigo/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.jdt.ui.prefs
Doing this, I was able to migrate my syntax highlighting from Helios to Indigo
Once Michael Bosworth's answer helped me to some extend and I voted up. But now I see some obligation to answer it myself, because copying these two files are not enough. Let me explain why.
First, these files contains lines irrevelente to syntax coloring.
Second, syntax coloring for other editors are located elsewhere, for example, those of XML files are in
org.eclipse.wst.xml.ui.prefs
and those of HTML files:
org.eclipse.wst.html.ui.prefs
JSP pages?
org.eclipse.jst.jsp.ui.prefs
, etc.
Third, when we change font colors, usually we change background colors, line highlighting colors, etc. to get a clearer view of codes. This involves more files.
If we search *.pref files in path
/workspace/.metadata/.plugins
we can find all preferences files where we can locate all lines of coloring settings. But by copy-pasting all these files to another workspace can also trigger problems, for they are not exclusively syntax-coloring-related. Moreover, when we are switching between two versions of Eclipse, unexpected problems may arise.
So, the safest way is:
Create a new workspace if you don't have one.
Open all *.pref files we find in the workspace one by one,
Copy those lines containing color codes,
Find the same file in your new workspace,
Replace the color part by existing one. Or, set the colors in Eclipse, by assuming the corresponding options according to properties' name. All color codes are RGB based.
EDIT: (2017.02.24)
Eclipse Mars has a plugin Oomph, which can record your preference settings to provide seamless transmission of your preferences. When you activate it, every time you change a value, it prompts to ask you if you want to record it in Oomph, providing you the exact line in the corresponding file where your new value is stored. So, when you install Oomph, you can:
Change the settings of your font face, font size, background color, etc.
In the prompt windows of Oomph, take note of the location of your new settings. (Because if you tell Oomph to remember your settings, it will not prompt never again, so you may only see this windows once.)