Script looks almost right (hint you can use the code tags to get proper formatting for code stuff)
You might be running into trouble by looping through and doing them individually like that.
Can you try the following:
#select the meshes on the R side first, first then run
import maya.cmds as mc
import zBuilder.builders.ziva as zva
zObj = zva.Ziva()
zObj.string_replace( '^R_', 'L_' )
zObj.string_replace( '_R_', '_L_' )
With the code you had, you might have been replacing any instance of 'R' with 'L' including ones that appeared in the object name which weren't to do with denoting left or right.