Media Clips and log notes disappearing.

Set my project up; created bins and all organised; start making a sequence and editing away. But after a while I go back to the bins and all the media clips that are not associated with media clips on the time have disappeared! So the only media remaining are to do with clips associated with clips on the time line.
Keeps on happening.
Thanks William

Thanks SO much for the responses they have been extrememly helpful.
What I'm trying to accomplish is...
I have all my home videos transferred onto sequentially numbered one hour mini-dv tapes. These tapes are the media I will be drawing from for almost all video projects I will be creating.. so rather than import from tapes for each project, I want to import all my video as quicktime media files onto my external hardrives and use these same media files for all projects. I want to set up a logically named and structured system for these all inclusive media files and have them logged for content in such a way that I can find any clip I need by searching (either in FCP or in spotlight).. I want all media files to contain the time code that corresponds to the original tapes so that recapture from the tapes is possible if it should become necessary.
My thoughts so far are that I would like each media file to be representative of one scene and labeled yeardatetape# (example 19970204_36B for second scene taking place on feb 4 1997 captured from tape 36), although I haven't ruled out having longer media files that cover more dates or possibly an entire one hour tape.
What I've found so far is that I'm unable to capture an entire tape without it stopping (due to slight glitches in tape and camera issues). What has worked best so far by trial and error with my equipment is to log a clip for each scene on the tape.. making sure to leave about 4s of intro time at scene start if tape is glitchy and then batch capture all the logged clips. So far I'm entering information about the scenes content in the log notes but I dont know if thats the best place.
I have several questions regarding media management that come up as I try to figure out my system for logging and capturing. Since this is a big undertaking (about 70 hours of video to capture and log) I'd like to come up with the most logical way to accomplish my goals and only do this one time!
Thanks again for the help!

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