I get something similar but with the .DAT flight logs not the .txt flight logs.In my case the small, second file is almost always from the start of the recording.
I use multiple phones and I don't keep the smaller DAT but I get the impression this happens on certain phones and only on those phones. The others record just one .DAT.
That is quite strange since the phones are all Samsung S6, though there are different memory sizes. I am not bothered by this peculiarity so I have not investigated the matter further.
If an Android phone it might be worth trying a different version of the App or uninstalling it and reinstalling it. With an iPhone I assume you can uninstall the app but you are, I believe, stuck with installing the current version of the app.