[AtlUmpSteve]

You have few options.

1) Call the out, as it technically violates.
2) Say you didn't see it, can't call what you didn't see. Hear some grief, but if you can support that possibility (more specifically to a momentary step off to tie a shoe or pull up a sock or knee pad), that might be your best answer.
3) Say you called time (needed to sweep a base or something equally foolish), so it didn't happen during live play.
4) Say you or your partner put the runner in jeopardy by changing or delaying a call.

It (#4) is the only legal way during live play to cover it up. You cannot use "spirit of the rule" which contradicts the rule. Only you and your partner (and a UIC) can know you really didn't put her in jeopardy; but if you are determined to protect her, and can't claim you didn't see it or called time, this may get you some grief, but it is generally protest proof (Mike may see through it, other UIC's may not like that explanation, but it passes muster if you think you could/should have ruled more clearly and timely).