A perfectly valid-looking CSV can delete every variant on a product.

A SKU or Weight column without Option1 Name and Value makes Shopify replace variants with one default variant. Check before importing.

The dangerous column combinations

These combinations are the ones that delete variants:

Variant SKU filled but Option1 Name and Option1 Value both empty.
Variant Grams (weight) filled without option columns.
A mix where some rows have options and others do not - the optionless rows get rebuilt.

ShopTools' validator checks every row for the variant-deleting combination - SKU or Weight without option pairs - and reports it before you upload.

Open the file and confirm every row with a SKU or Weight also has Option1 Name and Option1 Value.
If a product has no options, leave SKU and Weight empty on its rows.
Run the file through a validator that flags this exact combination.
Test the import on a development store if the catalog is large.

Before: Row: Variant SKU=SHIRT-L, Option1 Name=(empty), Option1 Value=(empty) After: Row: Variant SKU=SHIRT-L, Option1 Name=Size, Option1 Value=L (or leave SKU empty)
Before: Import 'succeeds' but product now has one default variant After: Import keeps all 6 size variants intact

Anyone re-importing product CSVs: Re-imports are where existing variants get wiped
Stores with many variants: Larger variant matrices = higher data-loss risk

Can a valid CSV really delete my variants?: Yes - Shopify's documentation says a SKU or Weight column without Option1 Name and Option1 Value rebuilds the product with a single default variant, deleting the rest. The import reports success.
Why does Shopify do this?: Variant-level columns without option columns are interpreted as a single default variant. Shopify rebuilds the product to match what the file describes.
How do I prevent it?: Ensure every row with a SKU or Weight also has Option1 Name and Option1 Value. If the product has no variants, leave SKU and Weight empty.
Can ShopTools detect this?: Yes - it flags the exact combination (SKU/Weight without option pairs) before you import, the check Shopify itself does not warn about.