Yep, I can confirm the issue was a stray Cursor.visible = true; left over from earlier in development that would trigger whenever you unpause specifically. Like you said not gamebreaking but the fix is as simple as deleting the line, so I went ahead and updated the windows build, and will update the linux build momentarily.
Your save data is stored separately from the game files, so you should be able to safely replace the old game with the new version. Just delete the old game folder, download the newest zip file for your machine, extract, open and launch the game, and the cursor issue should be fixed.
Thanks for letting me know so fast!