"No. The one and only thing I use one QThread is..."
euhm, that should be a 'yes (but it's disabled at the moment)'

Just because you do things with signal/slot doesn't mean that you are protected against threading issues when writing to text file.

From the symptoms, it feels like there must be multiple things opening the file. You also say 'sometimes whole line missing...' which implies you can't consistently repeat the issue. This also hints at multi threaded cause.