Yes you can.

You could use the ANT 'native2ascii' task to be executed automatically
with Eclipse.
The following are simple steps to follow with Eclipse 3.1 and a JDK
(1.4+) already installed.

1- Start Eclipse 3.1 with a JDK (not a JRE).
  To be sure, just before starting Eclipse, edit 'eclipse.ini' file in
{ECLIPSE_HOME} folder
  and put in the two first lines the two following lines:

-vm
{JDK_HOME}\bin\javaw.exe

  This example works for Windows.
  Of course {JDK_HOME} must be change appropriately for the JDK root
folder path.

2- In yur project, make sure that all your property files :
      a- are located in 'hebrew_properties' sub-folder
      b- have the '.properties' file extension
      c- are saved with the appropriate encoding (for instance
'ISO-8859-8' encoding).
         To be sure, open each file, then 'File' / 'Properties', then
check with the 'text file encoding' section.

3- In the root of your project, create a new file that you could name:
'convert_properties.xml'
  and with the following content:

<project name="convert_properties" default="convert">
    <target name="convert">
       <native2ascii encoding="ISO-8859-8"
                     src="hebrew_properties"
                     dest="WEB-INF/classes"
                     includes="**/*.properties"
       />
      </target>
</project>

4- Right-click on your project, then 'Properties', select 'Builders' in
tne left, then 'New' and 'OK' ('Ant Build' is pre-selected).
  Change the 'Name' field for 'convert_properties', then for
'Buildfile' click on 'Browse Workspace...' and select the
'convert_properties.xml' file.
  Then click on the 'Targets' panel, in 'Auto Build:' section click on
'Set Targets...' and then 'OK' ('convert' is pre-selected).
  Then click 'OK' and again 'OK'.

This should work fine and smoothly.
Of course you can change the folder names / files extensions / other
names at will.

Regards