No. Save data is stored separately (on NAND or cloud). However, some v1.0.1-to-v1.0.2 updates may disable cheats or mods that relied on older memory addresses.
If you follow the steps and match Title IDs, installing FF Pixel Remaster updates on a modded Switch is straightforward. For a clean, legal experience – just update via Nintendo’s servers on sysNAND. final fantasy pixel remaster switch nsp update install
Below is a generic, safe workflow for updating any of the six Pixel Remaster titles using an NSP update file. This process applies whether you are updating FFIV or FFVI . final fantasy pixel remaster switch nsp update install