Jimmie, I don't think how much free space you have will have much to do with how safe a particular file might be. Since there is no fragmentation on Linux-based DVRs, there is also then no extents file to get corrupted, which is the chief reason why fuller HDDs on Windows are more susceptible to files becoming corrupted and to fetching the files slower.
For a DVR, any one file is pretty much like any other, regardless of how many files there might be. The odds of any file on the HDD getting corrupted are about the same regardless of what else might be recorded anywhere else, or whether anything else is recorded at all. And having something stored in location A really does not impact storage location B, other than regarding the actual size of the database, which means it has no real impact. FIles recorded on my DVR have as much affect on files on your DVR as do other files on your DVR. IOW, none.
So what would be my guess here, is that the database record for that particular show got corrupted and can not link to the media file. When you reboot, the sanity check which audits all files against their database records, will mark that space as available for new recordings, meaning it is effectively erased.
This can happen if the HDD develops a bad spot, and I would worry about other shows disappearing if that is the cause; you really do not want a bad spot to develop over the top of DB records. It can also just happen spontaneously over time from bit rot, which, incredibly enough, is caused by cosmic rays. No kiddin'. IIRC, a bit can get flipped from one to zero or vice versa about every 10 seconds or so on any HDD, and of course the denser the media, such as on a 2 TB drive, the more susceptible it might be.
So that is almost as scary as dust mites, another problem that is everywhere all the time but typically never really is severe enough to be problematic. Bottom line, if you have a HDD, bits are getting flipped all the time. And this is something all HDDs are susceptible to; there isn't much that can stop a cosmic ray. But the odds of a relatively important bit or one that does not have error correction backing it up getting flipped, are pretty tiny, so lots of bit rot happens all the time; it just is not typically a problem. At least until the wrong bit gets randomly flipped.
But it is not a matter of if you will lose a particular recording on a HDD, it is a matter of when. Spinning HDDs are just not a reliable archive medium, and each has a real shelf life. They make a good cache medium, which is what a DVR is supposed to be, but permanent storage is, well, just isn't. The sad part is we are somewhat forced to utilize them to archive our media because as consumers we don't really have a better option.
So, I double record everything that is important on separate DVRs, and if I have something I need to save, I burn it to a DVDRW+, which is SD but still high quality if coming from HD, and maintains 16:9. Not perfect either, but better than losing something important.