That is a problema with the Luma Updater and as nothing to do with you're Luma3DS CFW. If youdid what I told you, your Luma3DS will be on the latest release without problems.I have started "Luma Update" and saw red signs under "current version" instead of the current version (6.3).
Luma Update said there is a new update available so I tried to download it. After download and reboot I am getting the configuration screen where I can choose the points u said like "3ds cpu, show sysnand, etc"..
After saving the settings I just checked the current version of Luma by restarting the Luma Update tool again and there is a note that says "Configuration not found, using default values" and there are still those red signs instead of the current version and there is still a new version available". I dont get what I did wrong.
Untill 6.3 there were never issues like now.
I think I did something wrong by installing the cfw and thats the result. Thats why I asked for a guide to reinstall the whole cfw new and clean without any mistakes.
There were reports of the updater having issues and some people changed to Star updater for that reason.
All in all, as long as your console is working properly, those red symbols are cosmetic and won't do any harm to the console.