The microsclerotia should be pretty resistant to surface disinfection with 10% chlorox for better isolation of soybean Macrophomina.
In addition to using more aggressive surface disinfection protocol try to take the sample from the edge of the focal lesions.
The areas away of from soil will be best such as advancing stem lesions.
Before disinfection really wash the material to eliminate all soil traces some detergent may be helpful.
When isolating initially take a single microsclerotia and let it germinate on moist sterile filter paper aseptically.
Isolate from the hyphal tips off the germinating microsclerotia.
I would not recommend trying to purify cultures that are mixed but rather getting your original source material so culture are pure avoiding the issues and added efforts.
From my experience getting away from mixed cultures soil is problematic.
This depends on the speed of growth of Macrophomina faster than Fusarium or by increasing the incubator temperatures to 35 degrees where the fungus Macrophomina , fusarium
can grow while Fusarium fungus can not grow and can then purify the fungus