Our Variants feature has been working "as advertised" for years now, with a significant number of our 6700+ merchants using it happily, so we'd be glad to help you get it set up correctly to accomplish what you need. Variants lines disappearing suggests that something wasn't configured right, so it simply removed any lines that it couldn't interpret as meaning anything.
At the top of the Variants config screen, you would give a suitable name for up to three menus the buyer would be shown. E.g., the Option1Name could be something like "Size", the Option2Name could be something like "Color", and the Option3Name could be something like "Style". Below that, you would define every possible Variant using the options you offer in those categories. Bear in mind that each line in Variants defines a SPECIFIC COMBINATION of option values, with details for each combination given in this exact order:
The option menus shown to the buyer take their values from all of the Variants lines for each OptionXValue position. The first menu would show all of the Option1Values from all lines, the second menu shows all of the Option2Values, and the third menu shows all Option3Values. For instance then, let's look at this example line:
For some imaginary product named "Garply", that line defines the specific Variant combination where the buyer chooses a size Medium (first menu), which is Red (second menu), and Short (third menu); that Variant combination costs $29.99, weighs 5 oz. for shipping, and has 32 units in stock for inventory.
Everything up to the first comma on each line is treated as the SKU for that line. E.g., the specific combination above is identified with the unique SKU (stock-keeping unit) code of "Garply MRS". The SKU must be unique for each line and can be anything you want to help you identify exactly which combination was ordered (e.g., if you already have your own stock-numbering system, you could just use that for your SKUs).
If we're not using Inventory Control nor weight-based Shipping calculation, that example line would look like this (note how we've left the Weight and Stock positions empty), and let's add some lines for other sizes while we're at it:
Once you configure every possible Variant like this, the Add to Cart button code we provide to you for that product would automatically include the necessary menus for the buyer to select.