Verdict: Yes
Yes. MEGA builds its desktop app for Linux as well as Windows and Mac, and officially supports Debian, Ubuntu, Mint, Fedora and CentOS, so your synced folders carry straight over.
The MEGA desktop app source and its own documentation list Windows, macOS and Linux, and name Debian, Ubuntu, Mint, Fedora and CentOS as the officially supported Linux systems, with prebuilt packages for several others offered on the MEGA desktop download page. For most home users that covers whatever they have chosen.
Setting it up again is the same few steps as on Windows. Sign in, choose which folders on your computer should match which folders in MEGA, and let it catch up. Because your files are already in MEGA, the app downloads them onto the new machine rather than you having to copy anything across by hand.
Two things to sort out before you wipe Windows. First, make sure you have your MEGA recovery key saved somewhere else. MEGA encrypts your files with your password and cannot reset it for you, so losing it loses everything. Second, if you had paused syncing on some folders, check they finished uploading.
Be patient with the first sync on Linux. A large account can take days over a home connection, and it is normal for the icon to sit there working for a long time.
Only relevant if you want to leave MEGA. Same folder syncing idea but you or a provider host the storage.
Your files: No MEGA import. You would download your files from MEGA and upload them once.
Copies folders directly between your own computers with no cloud in the middle. Free, private, but no online copy to fall back on.
Your files: No MEGA import. Works on plain folders of files.
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