Hey Marion,

This one is a slightly thorny problem, there are a few relevant parts of the manual that you should look at first.

The 1NT opening was 15 to 17 points, the 2NT overcall by S showed both minors

If we look at page D58 of the NZB Manual, we see the following:

• 29.2.4 Self-alerting calls defined
  There are four different types of self-alerting calls, namely:
  • doubles;
  • redoubles;
  • cue bids of an opponent’s denomination/suit;
  • all conventional bids at the four level or higher but excluding conventional opening bids on the first round of the auction (these bids still require an alert during the auction).

This shows that North should not alert 2NT, regardless of the meaning; as it is a cue bid in the same denomination as the opponents had opened. (If North overcalled 2S for the minors, then this should have been alerted).

which was not alerted by partner who was not sure about the meaning.

Aside from the above stating that any cue-bid is not alertable, we now look at page D61 29.8 [so I'm going to 'run' with a parallel example of a 2S overcall which has the same meaning]:

A Player may not be sure whether a call should be alerted. This could be because the Player has forgotten the agreement, has forgotten whether there is an agreement or is unsure whether an agreement applies. In such cases, it is generally safer to alert the call and, if asked, explain the circumstances. However, the uncertainty about the meaning of the call is unauthorised information to the Player’s partner.

So if South had overcalled 2S (both minors), and North still wasn't sure; then North should alert 2S and say "we haven't actually discussed this bid, but we have discussed that a 2D overcall would show a natural 2S overcall" [or whatever is causing them to doubt the fact that it's a natural bid].

Now let's fly back up the page to B12:

A Player whose conventional call or special treatment has not been alerted by partner should not make any attempt to alert the opponents until the close of the auction. Before the opening lead is made, dummy or declarer should call the Director and inform the opponents of the failure to alert. However, a member of the defending side must wait until the conclusion of play, summon the Director and draw attention to partner’s failure to alert (Law 20F5(b)).

So during the auction, South shouldn't stare intently at North until they "wake up" and alert 2NT [or the fictional 2S equivalent] (as people at the table presumed should happen). After the auction and before the opening lead; North/South should explain that either 2NT showed both minors (a delayed alert - typically indicated by a small cross on the bidding pad above the bid in question), or South should draw attention to the failure to alert the 2S overcall.

Because 2NT isn't alertable, E/W have no redress here.
If there was a 2S overcall, then E/W would have redress under Law 21.

LAW 21 - MISINFORMATION
A. Call or Play Based on Player’s Own Misunderstanding
No rectification or redress is due to a player who acts on the basis of his own misunderstanding.
This does not apply.
B. Call Based on Misinformation from an Opponent
1.
(a) Until the end of the auction period (see Law 17D) and provided that his partner has not subsequently called, a player may change a call without other rectification for his side when the Director judges that the decision to make the call could well have been influenced by misinformation given to the player by an opponent. Failure to alert promptly where an alert is required by the Regulating Authority is deemed misinformation.
Because we're at the end of the auction period, this does not apply.
(b) The Director is to presume Mistaken Explanation rather than Mistaken Call in the absence of evidence to the contrary.
The director should examine the system card of the offending pair; and see what the 2S [2NT analogue] call meant.
2. When a player elects to change a call because of misinformation (as in 1 preceding), his LHO may then in turn change any subsequent call he may have made, but Law 16C applies.
As we're out of the auction period, this doesn't apply.
3. When it is too late to change a call and the Director judges that the offending side gained an advantage from the irregularity he awards an adjusted score.
The meat of the question, one needs to judge if E/W were damaged here. This is what you'd apply.

The important thing to remember when considering this board, is that the "legal" actions on the board need to be maintained. It is "legal" for South to have overcalled 2NT [2S] both minors; the infraction lies in the alert. There would be damage if it was conceivable that E/W could compete to 3S which would make, but without the alert it would be hard for them to do so.
There would be damage if declarer didn't explain the failure to alert / post-alert their 2S/2N overcall and the East chose a poor opening lead when they would have made a different lead had they known (e.g. they lead a D from their sequence and started setting up dummy's second suit, when they could have lead a safe H instead).
There would not be damage if EW+50 is the best conceivable attainable result for the EW pair after the 2S/2NT overcall. East/West are allowed the benefit of the doubt, but imagining that it "looks" like 3C should comfortably make and that defeating it is a fluke, you wouldn't award them 3Cx-1. If one of the defenders has a lot of minor honours sitting over the 2-suiter, you could see them attempting to penalise the opps; assuming that X from them would be penalties and you likely would adjust the score to 3Cx-1.

I concur with what Brad says here but would add:

Often the best thing to do in this situation (that is one is not sure what partner's bid means) is to have North leave the table and South explain the agreement about his bid to the oponents only

That doesn't apply if there is NO explicit agreement
In that case all 4 players have to guess and either side could get lucky

When there is no agreement any pertinent information should still be given in response to a question
Such as here North should say (if it is true!)
We play 2NT over a 1-(major) suit opening is for the minors 
and/or
We never bid 2NT over 1NT with a strong balanced hand; we double then

Thank you both Brad and Nick,

This was extremely helpfull

Cheers,

Marion