I have noticed this sometimes when recording MIDI notes, but I have no idea why that happens. It might have been a bug in a previous version of FL Studio that is fixed in the current one. I'm frankly not up to date with the latest build yet, so I cannot tell for sure; but I would recommend updating to the latest version and see if the problem still persists when recording.
However, there might still be a way to recover your data: If the audio you recorded was written to your storage device, it should be located in the directory named 'Recorded' in the browser. Also, in the case of recording MIDI notes, if you did that one perfect performance and it suddenly went to nowhere, you should be able to retrieve a score log from the Tools menu by hovering down to 'Dump score log to selected pattern'.
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