Delete variations on eBay listings in bulk!
Navigate to: Products → Listings Manager → CSV Import
Use the 3Dsellers Update Listings via CSV feature:

Step 1 - Create a CSV
In your CSV, include at least these three columns:
SKU (the main listing's SKU)
VariationSKU (the variation you want to delete)
DeleteVariation
SKU | VariationSKU | DeleteVariation | Price |
MAIN_00 | |||
VARIATION_1 | TRUE | ||
VARIATION_2 | 24.99 |
To remove a variation, set the DeleteVariation cell to TRUE
The example CSV above will delete VARTIATION_1 and change the price of VARIATION_2 to 24.99
Mapping Identifiers
In step 2 of the upload process (more info on steps 1 and three), use the following settings:
Update item by SKU
SKU Column: your variation SKU column
Variation's Parent SKU column: your column for the main listing's SKU

After completing the mapping and upload, variations with DeleteVariation fields marked as "TRUE" will be removed from eBay.