Try editing plugins/woocommerce/includes/class-wc-ajax.php around line 894 max variations from 49 to say 299.
You may need to increase memory limits also as creating variations will take allot longer than when it was set to only create 50 varitions at ones.
I had tried adding the filter at wp-config and funtions.php and also tried the theme functions.php but they didnt work so editing the file directly seems to work.
If you can find the class-wc-ajax.php you can run a search for 49 and it should take you to the line that the limit is set.
Be sure to back up any file you work on incase it breaks the site.
