EPS files open with unusual line slices

We have roughly 4500 eps files that were created in freehand years ago. The files contain both raster images that were embedded as well filled vector paths which were created in freehand. The embedded raster image opens flawlessly as wells as some of the filled paths. I say "some of the filled paths" because there are other filled vector paths that were created using the freehand auto-trace function (similar to AI's live trace)- these filled paths open incorrectly. They open with unusual lines that perforate the entire filled object- a strange slicing effect that appears to happen only to the filled paths that underwent freehand's auto-trace function. The other art appears to be fine.
Is there a method to correct this problem in AI? I'm using A mac os 10.6.8 cs5, When I open the eps in photoshop I don't see any slicing- but photoshop also converts it to a raster image and I would like to preserve the paths. When I open the image again in freehand it opens fine.
Below are examples showing the sclicing effect.

Hello Mike
Yes, I was able to arrive at that solution as well- converting the paths to a raster image then running a live trace on that raster file. I haven't tried uniting the paths though... good suggestion! Thank you!
The only solution I found so far to keep the eps in a proper vector format was opening the "corrupted" eps in illustrator and selecting all paths and convert that selection into raster art, then convert the raster art back into vector art (live trace). This action can be automated in a batch sequence (4500 files are a bit to much to open individually). The lines will vanish! However the paths will all be one layer with varying color (color differs depending on the artwork), not ideal but it is the best solution that I can think of.
Do you know any way to release the paths after you preform the live trace function. It seems (in the case of multiple colors especially) that when a raster image undergoes the live trace option the end result is one object with multiple paths that appear to be grouped together. Is there any way to release these paths? So one could identify them separately by mousing over them?
Thank you for your help.

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