Will my skins shards be affected by new season?

Are you making any changes to the way disenchanting shards works?

Since you'll be getting more shards thanks to the new leveling system (and with other recent changes to honor and events), we'll tune down the relative value of the essence you get from disenchanting shards of all types—champ shards, skin shards, and ward skin shards.

https://support.riotgames.com/hc/en-us/articles/115012640908-Preseason-Update-FAQ

You don't need to get rid of your champ shards. Champ shard values are decreasing, so riot explained that if you're planning on disenchanting them, you should do it sooner than later. If you're holding onto them for the mastery level benefit, nothing is changing and you should still hold onto them.

Nothing will happen to your skin shards. They won't decrease in value nor will you lose them.