Will you be able to access that file 5 years from now?
Some time ago, I made the decision to keep most of my documents and data in formats that would survive the passing of time.
Products get killed. That document created using an old version of Microsoft Office? Chances are it's incompatible with the latest Office version, Maybe you won't be able to open that mind map that took you hours of work, if the software you used to create it no longer exists. How about Google deleting your account?
I keep the notes I take--my second brain--in plain-text format. Facts can be easily checked using the internet. However, insights and notes product of reflection and deep thinking may be impossible to recover if lost.
From plain text editors to great apps like Brett Terpstra's nvAlt, to specific applications for building a second-brain like The Archive, Obsidian, LogSeq, Zettlr or even Emacs, there is no shortage of apps for handling text files. Most of these apps offer some kind of [[wiki linking]] to create links between notes. By using text files, the underlying information persists and is always accessible even if you change apps for whatever reason.
If text files are not for you, then at least make sure that the applications you use offer a way to export your data in a way you can migrate to another app easily[^evernote] without losing information.
[^evernote]: For example, Evernote stores your data in the cloud. Even if it's not directly accessible to you, Evernote allows you to export all your data in a format that's recognized by many applications.