If you have multiple charts in a file, you can select the chart you wish to delete by clicking just beyond the edge of the chart, in line with the row or column number labels, and then either use the X delete icon or open Edit in the main menu and select Delete. You can find more help on this by reading about Stitchmastery's Selection Tools and about Having multiple charts in one file.
If you wish to delete a whole chart file, use your computer's search function to look for ".knt2" which is the file extension that will appear on your chart file. That will help you locate the files. Alternatively, if you have the file open in Stitchmastery, hover your mouse over the tab which contains the chart's name, and the location will appear beside your cursor:
When you have located the file on your computer, you can delete it in the same way you would delete any other file - either click it to select and hit Delete on your keyboard, right click it and click Delete, or click and drag on it to move it into your Recycling Bin.