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Hi, you can flash the new rom with SP Flash Tool, but you will lose your root acces.
You can flash the new ROM, but you will lose your root acces, but you will keep any data and files.
If you flash the new ROM with SP Flash Tool, you actually flash a new system. But the new system that you flash doesn't have root acces, so you flash a non-rooted rom / system.
But if you only flash the "System.img" with SP Flash Tool, you will keep your date, but loose root acces. Hope I helped you 
If you have any questions, just ask them!
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