Can you provide an example ant build script (e.g. build.xml)?
In version 2020R2, the isCOBOL compiler was integrated in Apache Ant builds.
You can find an ant build script in the $ISCOBOL/samples/issamples folder, with instructions to implement it in the README.md in the same folder.
If you are using a version prior to isCOBOL 2020 R2, you'll find a generic example attached of a build.xml ant script to use with isCOBOL and ant.
Modify the directory and options properties at the beginning of the file, especially the one pointing to the iscobol.dir: