Csound does not allow filenames to be passed simply to Csound scores for usage in 'soundin' generators. This system gets around this by claiming the filenames soundin.1, soundin.2 etc for use (or sin1, sin2 etc on some systems.) This means that old files with these names will be removed by this program during its normal operation.
In summary, don't use these tools in a directory containing a file of form soundin.<n> (or sin<n>) that you want to keep.
Further, the version of Csound I am using (3.37) has a bug reading WAVE files with the 'soundin' unit generator - though perhaps it has been fixed in other versions. Csound does not recognise non-audio data blocks at the end of sound files and consequently reads them as audio, causing clicks at the end of sounds. This can be compensated for by explicitly setting a 'to' time just before the end of the sound to play back or by ensuring the soundfiles are saved without this data. A better solution would be to repair Csound itself.