Thank you for those details. While we do have certain limitations, which I will list below, that could affect your CSV import you generally should be seeing an error message letting you know this is the case.
100 Variants per product.
If a shop has 50,000 variants then the variant upload limit is 1000 variants per day.
If those limitations have not been met then the next things to look for:
Are you receiving any emails detailing if the CSV upload failed?
What happens if you try to upload just a few lines/products from this CSV file instead of the whole thing?
If you aren’t able to resolve this issue then please reach out to our authenticated support team. In rare situations a CSV upload can get stuck, causing issues with further uploads. We have tools in place to help reset that and also review any possible issues or error messages in your CSV file. To access our authenticated support, please follow this link: Shopify Help Center.