When saving a capture containing more than 1M samples, the output is truncated to exactly 1M samples (1,048,576) when saving as CSV or text. The file save dialogue gives a plausible size estimate such as "saving a large file of approximately 76MB" but the file produced is a lot smaller, around 36MB for two channels.
I'm using Picoscope R6.8.10 and a 3404A scope but the problem is also present in demo mode so I doubt the model of scope is relevant.
That is an unfortunate limitation - not everyone uses Excel and there is no reason to bind everyone to its limitations.
I will investigate using the matlab format output.