The recommended workflow for FCP from RED’s website is to convert files using RED Rushes or Log & Transfer into ProRes QT files before editing, maintaining the same file names.
When you send these file to Color, they can be used to relink to r3d files. Using proxy files is not recommended, probably for the reasons you have discovered. Can you change the file names to remove the extra? Save, backup and duplicate before fiddling with file names.
Research, consult and test with any new workflow long before you hit the critical time with others are watching on and the clock is ticking. The RED website has lots of info and recommendations. Perhaps their forum will have already answered this question for you.