I would use the gen 8 files from the lowrider page. I added support to attach mechanical endstops in the updated files.
http://www.thingiverse.com/thing:4213
About your actual question, people say you can use netfabb's online stl repair tool to fix your problem. I've never used it myself though.
One thing you can also try is to change your layer height, if the slices don't hit the hole, you should be fine. Sounds dumb but it has worked for me in the past.
Best,
Aaron Double
twotimes
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