This is not a TVHeadend problem but an XBMC glitch.
I have found a workaround for the issue. I have added my RecordedTV folder to my Videos library in XBMC which does get updated even if the old recordings dissapear from the recordings list in XBMC.
I would also recommend that you change the way TVHeadend names files so that is adds the channel, date and time of the recordings to the file name so you can find them.
Please refer to the attached screenshot.