I only use batiks for hand applique and quilting and I don't have a problem.
I've never washed them first and they don't run when I washed the finished quilt. True batiks are made by putting the design on plain muslin fabric with stamps and hot wax. Then they are dyed. To get the wax off, they are boiled. No need to wash first or twice. If your fabric is bleeding and you have to wash it twice, it isn't a real bali batik.