The shape's color is defined by its FillStyle property. If this property is null, the shape takes its fill style from its template. Setting this property assigns a private fill style to the shape. Fill styles are part of the project's design and can be identified by their name. Standard fill styles additionally have a property in the Design class.
Identify the desired standard fill style in the design and assign it to the shape. For example the standard red fill style:
myShape.FillStyle = myProject.Design.FillStyles.Red;
When you assign an explicit private fill style to a shape the fill style is detached from the template and future changes to the template's fill style will not affect the shape anymore. To re-attach the shape's fill style to the template, assign null/Nothing to the shape's fill style.
Identify the desired fill style through its name and assign it to the shape. For example a custom fill style named MyNewFillStyle:
myShape.FillStyle = myProject.Design.FillStyles["MyNewFillStyle"];
Above notes apply here as well.