Are you using the latest version?
I just verified that the latest version *does* set the "is dirty" state (that causes the * in the title and the Save As to be highlighted) when flags are modified.
For the majority of items TiTS only uses 4 fields for saving information about items: shortName, classInstance, quantity, and version.
So any changes to stats won't be loaded from the save.
There isn't a single "knob" for that.
Cum quantity is a calculated value based on several fields including ball size, ball efficiency, ball fullness, and cum multiplier.