Hi,
This probably means that there is a problem with the CSV.
In it, you need to have first one row for the main product and one row for each variant.
You also need the product_code column (for the code of each product / variant) and the product_parent_id column (with the code of the parent product for variants).
You also need one column for each characteristic, with the value of the characteristic for each variant.
This is required if you're using the Products>Import menu, even if the products and variants are already in the database.
That's because the system will delete the links between the variants and the characteristics to recreate them so that a CSV import can delete the variants that are in the database but not in the CSV anymore.
If you want to simplify the CSV update of variant prices, you should rather use a mass action with a filter "import from CSV file". With this, you can just provide the product_code column and the price_value column to update the prices without having to take into account the characteristics, etc.
However, now that you've imported a CSV file with missing information for the variants, the data of the variants in the database is messed up. The ones you don't see are still in the database, but not linked to a characteristic / value. So to fix everything, you would have to fix the CSV file with the normal import first.