I noticed 2x2 duplicate trade IDs in the Z12 status page and apparently resulting wrong values for current price, risk, etc.:

Trade ID Lots Entry Time Entry Price Stop Trail Target Risk Profit Pips
[AUD/USD:NET:S1501] 3521501 3 29.08. 00:14 0.753 0.7685 1.0542 - - - - - - - - -8079$ -413$ -154.1p
[XAU/USD:NET:L5440] 3525440 1 29.08. 20:14 1323 1350 926 - - - - - - - - -3553$ 236$ 2643.2p
[XAG/USD:NET:S1212] 3531212 1 30.08. 16:14 18.655 20.07 26.12 - - - - - - - - -3359$ -638$ -142.3p
[GBP/USD:NET:L5090] 3545090 2 01.09. 12:09 1314 1350 0.9276 - - - - - - - - -23559869$ 319$ 177.7p
[EUR/USD:NET:L5089] 3545089 1 01.09. 20:09 1.1201 1.1252 0.7841 - - - - - - - - -3002$ 43$ 48.7p
[XAU/USD:NET:L5090] 3545090 1 01.09. 20:09 1314 1350 920 - - - - - - - - -3523$ 319$ 3572.0p
[EUR/USD:NET:L5995] 3545995 2 02.09. 00:09 1.12 1.1252 0.784 - - - - - - - - -6004$ 89$ 49.7p
[USD/CAD:NET:S5490] 3565490 1 02.09. 16:03 1.3431 1.3427 1.8203 - - - - - - - - -3293$ -2$ -2.7p
[USD/JPY:NET:S5122] 3555122 2 05.09. 12:03 103.27 102.07 144.58 - - - - - - - - -7174$ 209$ 120.1p
[GBP/USD:CY:L4238] 3564238 1 06.09. 14:37 1.3426 1.343 0.9399 - - - - - - - - -3612$ 1$ 1.2p
[EUR/USD:NET:L4898] 3564898 1 06.09. 16:20 1.1241 1.1252 0.7868 - - - - - - - - -3002$ 9$ 9.9p
[GBP/USD:NET:L5490] 3565490 1 06.09. 20:20 1.3429 1.3429 0.9401 - - - - - - - - -3583$ -2$ -2.1p
[USD/JPY:NET:S5492] 3565492 2 06.09. 20:20 102.01 102.07 142.82 - - - - - - - - -7114$ -11$ -6.3p
{AUD/USD:CY:s4502} 54502 3 29.08. 00:14 0.753 0.7684 0.7757 0.7303 - - - - -614$ -432$ -161.2p
...

In the MT4 Trade window both trades are having different and unique Order IDs (1st GBP/USD: 3542722, USD/CAD: 3550943).

Any ideas how this could have happened and/or how to diagnose further?
As far as I remember, I might have experienced a crash/reboot of my VPS, so maybe it relates to a buggy Z12.trd file. Any general recommendations how to recover from such a situation - without closing all trades and restarting completely fresh?

Close all 4 trades in the MT4 console. The other trades may stay open. The positions will be automaticalle re-adjusted by Zorro when a trade with that asset is opened or closed the next time. - We had already a report by another user with the same issue, also after a VPS crash. We're currently checking what exactly happened and how it can be prevented.

In MT4 the MagicNumber can be used to prevent duplicate orders/positions.

Here is a piece of code that I use in my RangeTrader to find all orders/postions after a restart:

void Synchronize( int MagicNumber )
{
for ( int Count = OrdersTotal(); Count > 0; Count-- )
{
if ( OrderSelect( ( Count - 1 ), SELECT_BY_POS, MODE_TRADES ) != true ) continue;
if ( OrderSymbol() != Symbol() ) continue;
if ( OrderMagicNumber() != MagicNumber ) continue;

switch ( OrderType() )
{
case OP_BUY :
case OP_BUYLIMIT :
case OP_BUYSTOP : Trade.Long = OrderTicket();

break;

case OP_SELL :
case OP_SELLLIMIT:
case OP_SELLSTOP : Trade.Short = OrderTicket();

break;
}
}

LogTicket( Trade.Long, "Synchronize(Long)", ERR_NO_ERROR );
LogTicket( Trade.Short, "Synchronize(Short)", ERR_NO_ERROR );
}

Again I have a duplicate Trade ID ... this time I'm sure there was no issue with the VPS. While it might be challenging to ultimately fix this it would be good to provide a way of automatically watching for such duplicates and throw an alarm once it happens.
(Otherwise Z12 is working quite well recently ...)

Yes, we'll detect duplicate IDs in the next version, 1.52.

Had another one. Maybe the duplicates are somehow related to a partial close? See below.

In MT4 the GBP/USD position is dated 2016.09.15 09:07:48 and the US30 position is dated 2016.09.15 13:07:47. Time difference between broker's server and VPS is 2h: UTC vs. CEST (when starting the strategy Zorro reported !MT4 time zone shift -1 at UTC ... is this the reason why the time difference between the trade open timestamps in MT4 and Zorro is just 1h ?). I'm running Zorro S 1.46.3. Maybe this helps.

Friday 16.09.16 Profit +786$ ----
{GBP/USD:ES:s9934} Cover 6@1.3237: -122$ at 00:08
{GBP/USD:ES:l0337} Long 5@1.3237 Risk 1011$ .
[GBP/USD:NET:S0426] Cover 3@1.3237: +51.07 at 00:08
[GBP/USD:NET:S3806] Cover 4@1.3237: -147$ at 00:08
[GBP/USD:NET:S7488] Cover part 4@1.3237: +115$ at 00:08..................................................

[Fri 16.09.16 04:08] 14847 +3586 +799 !6/4...................................................................................
[Fri 16.09.16 08:08] 15038 +3586 +906 !6/4
{EUR/USD:HU:s0538} Short 4@1.1237 Risk 1221$ ts.
[EUR/USD:NET:S4320] Short 4@1.1237 Pool trade........................................................................................................................................

[Fri 16.09.16 12:08] 15218 +3586 +989 !8/3
{GBP/USD:ES:l0337} Sell 5@1.3174: -289$ at 12:08
{GBP/USD:ES:s0639} Short 6@1.3174 Risk 1197$ .
[GBP/USD:NET:S7675] Short 11@1.3174 Pool trade....................................................................................................................................


Trade ID Lots Entry Time Entry Price Stop Trail Target Risk Profit Pips
[EUR/USD:NET:S1108] 3581108 16 09.09. 00:08 1.1265 1.1157 1.5772 - - - - - - - - -64022$ 1547$ 108.9p
[XAU/USD:NET:L1513] 3581513 2 09.09. 04:08 1339 1309 937 - - - - - - - - -7130$ -536$ -3019.8p
[UK100:NET:S2557] 3582557 3 09.09. 08:08 6853 6720 9594 - - - - - - - - -9707$ 464$ 1311.8p
[EUR/USD:NET:S7579] 3587579 8 12.09. 00:08 1.1238 1.1157 1.5733 - - - - - - - - -32011$ 575$ 80.8p
[XAU/USD:NET:L8720] 3598720 2 13.09. 08:08 1331 1309 932 - - - - - - - - -7116$ -392$ -2203.4p
[SPX500:NET:L1317] 3611317 1 14.09. 16:08 2134 2137 1494 - - - - - - - - -14213$ 73$ 328.2p
[XAU/USD:NET:L1318] 3611318 2 14.09. 16:08 1324 1309 927 - - - - - - - - -7057$ -270$ -1518.7p
[AUD/USD:NET:L4900] 3614900 8 15.09. 04:08 0.7464 0.7489 0.5225 - - - - - - - - -15940$ 176$ 24.8p
[USD/JPY:NET:S4902] 3614902 4 15.09. 04:08 102.29 102.34 143.21 - - - - - - - - -14237$ -19$ -5.4p
[GBP/USD:NET:S7488] 3617488 2 15.09. 08:08 18066 18132 1.8502 - - - - - - - - +321737811$ 117$ 65.7p
[US30:NET:L7488] 3617488 2 15.09. 12:08 18066 18133 12646 - - - - - - - - -9640$ 117$ 658.4p
[EUR/USD:NET:S4320] 3624320 4 16.09. 08:08 1.1237 1.1157 1.5732 - - - - - - - - -16005$ 286$ 80.5p
[GBP/USD:NET:S7675] 3627675 11 16.09. 12:08 1.3174 1.3087 1.8443 - - - - - - - - -51637$ 842$ 86.0p
{EUR/USD:CY:s6804} 56804 4 08.09. 00:08 1.124 1.1157 1.1599 1.0882 - - - - -1280$ 292$ 82.0p

Which of the two trades has the correct ID in the MT4 terminal? The GBP or the US30 trade?

the US30 trade had ID 3617488 (in the meantime I have closed both trades)

Hmm, the trade ID normally changes when a trade is only partically closed, so that would be a hint why this happens - but it does not happen here when I test it. Maybe it is broker dependent. Which broker are you using?

I'm using IG here. But I will transition to FXCM soon to get Microlots and rid of the MT4 requirement. Nevertheless, I would be happy to support debugging if you let me know what additional data you need and how to capture. I had such duplicates now 3 times in less than 4 weeks trading Z12, so a "good" chance to capture another event soon...