See also the discussion about the Invisible and Mask traits at the thread Double Blind capability?. Getting those two traits right is not straight forward, and their capabilities does not always live up to expectations.
As others have correctly pointed out. making the piece image(s) semi-transparent (half-transparent: opacity=50%, alpha=0.5, fully transparent: opacity=0%, alpha=1, folly opaque: opacity=100%, alpha=0), is a good solution.
Also consider to put those kind of markers on a different Game Piece Layers. That can prevent them from showing up in stack viewers, not be selected when drag-selecting (see also Does not stack), and so on.
For an example, see for example Gettysburg: 125th Anniversary Edition, D-Day - Smithsonian Edition, or Battle of the Bulge - Smithsonian Edition. These modules contains fixed control markers that can be toggled but are on a low layer and cannot be moved, nor selected in a normal fashion.
Note, this would still be limited by the problems explored in this reply - That is, if side A made a piece invisible, then side B cannot toggle the invisibility.
Yours,
Christian