Deleting alternate index (.AIX) or path (.PATH) from ESMAC also deletes the base file. Shouldn't this only delete the alternate index or path, and not the base file?

On the mainframe, the VSAM files are organized in a way that each alternate index entry (i.e. AIX, PATH, etc.) is associated with its own file while on Micro Focus Enterprise Server, all these alternate index entries are by design pointing to the same file, which is the base.
 
For this reason, it is not recommended to use the Catalog View to delete these entries. You should use instead a JCL to delete them, which will not cause to delete the base's physical file.