Re-naming clips/reconnection

Hi there,
I've got an incredibly important project and I'm getting into a bit of a muddle and stressed about backing everything up and sorting out the files.
Bit of background of what I'm doing....shooting in AVCHD, ingesting into FCP through Log & Transfer, and through Compressor I'm converting the clips to DV to work with in the edit.
I have a DV folder with all the converted clips which I bring into FCP and work away with. My question really is that I was going to use the 'rename - file to match clip' setting to change all the file names because there are a couple of Clip 1's and Clip 2's etc which I don't want confused. For ease of use I thought it best to change the names.
I've researched and seen there is some horror stories with reconnection issues changing names of files. I've got a back of the original cards on one drive. I've got a main project drive with everything on it and another back-up project drive which is a clone of the main one.
My question is this really, if something went horribly wrong where both the main drive and back-up drive died on me, and I only had the original cards left with a project file - surely there would be problems reconnecting? The ingesting and conversion process I'm sure would mean different file names......and if I had do go ahead and change the file names in this project how would it be able to reconnect properly? For example, if Clip No.1 was changed to 'Tom in Car' and I had to go through the ingesting/conversion process again, I would then have to find the relevant Clip No 1 and change the name again to 'Tom in Car' and do this similarly for every clip in the project??? And that would reconnect again? Is that right?
Sorry I'm beginning to confuse myself.
I'm basically trying as hard as possible to not mess this up, so if anyone could offer some advice or if I'm doing anything incredibly idiotic then feel free to correct my stupidity.
Thanks guys

That's a good suggestion, I'll start doing that.
One thing though, with ingesting often I'll have a couple of Clip 1's, 2's, etc - a Log Note or Label Note won't help differentiate the files if reconnecting though would it?? How will it know which file it's supposed to be reconnecting to..
There are a lot of files on this project thus far and so I just log and transfer them all in and then sort them out when they're in FCP....unfortunately this means a lot of duplicate filenames. Really bad practice methinks, I'll need to read up a bit more on this process.

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