After quite some digging I have been able to isolate the source of the problem to a custom feature that allows the user to get a shipment quote before they checkout. At the moment my best guess is that the call to PackageBasket in order to get the quote is what is clearing the basket contents?

Here is the API method I am calling:

[System.Web.Http.HttpGet]
public UpdatedSaleSummary GetShipRateQuote(string customerToken, string countryCode)
{
    var catalog = MerchelloContext.Current.Services.WarehouseService.GetAllWarehouseCatalogs().FirstOrDefault();
    var gatewayproviderService = MerchelloContext.Current.Services.GatewayProviderService;
    var country = gatewayproviderService.GetShipCountry(catalog.Key, countryCode);
    var tokenKey = customerToken.DecryptWithMachineKey();
    var customerKey = new Guid(tokenKey);
    var customerBase = this._merchelloContext.Services.CustomerService.GetAnyByKey(customerKey);

    var provinces = GetProvincesForCountry(country.CountryCode);
    var province = provinces.Any() ? provinces.FirstOrDefault().Code : string.Empty;
    var shipment =
        customerBase.Basket()
            .PackageBasket(new Address { Region = province, CountryCode = country.CountryCode })
            .FirstOrDefault();
    var quote = shipment.ShipmentRateQuotes(false).FirstOrDefault(x => x.ShipMethod.ShipCountryKey == country.Key);

    var checkoutMgr = customerBase.Basket().GetCheckoutManager();

    // Clear previous shipment quotes
    checkoutMgr.Shipping.ClearShipmentRateQuotes();

    if (quote != null)
    {
        quote.Rate = CurrencyHelper.ConvertToCurrency(quote.Rate, CurrencyHelper.GetCustomerCurrency());
        checkoutMgr.Shipping.SaveShipmentRateQuote(quote);
    }

    checkoutMgr.Customer.SaveBillToAddress(new Address { CountryCode = countryCode });
    checkoutMgr.Customer.SaveShipToAddress(new Address { CountryCode = countryCode });

    var invoice = checkoutMgr.Payment.PrepareInvoice();

    var summary = new UpdatedSaleSummary()
                      {
                          TotalLabel = "Total",
                          InvoiceTotal = ModelExtensions.FormatPrice(invoice.Total, this._currency),
                          TaxTotal = ModelExtensions.FormatPrice(invoice.TaxLineItems().Sum(x => x.TotalPrice), this._currency),
                          DiscountsTotal =
                              ModelExtensions.FormatPrice(invoice.DiscountLineItems().Sum(x => x.TotalPrice), this._currency),
                          ShippingTotal =
                              ModelExtensions.FormatPrice(invoice.ShippingLineItems().Sum(x => x.TotalPrice), this._currency)
                      };

    return summary;
}

The cart contents are actually being wiped out on the call to customerBase.Basket().GetCheckoutManager();.

I've tried changing the CheckoutContextSettings passed to the GetCheckoutManager() method but still, the problem persists:

var checkoutMgr = customerBase.Basket().GetCheckoutManager(
                new CheckoutContextSettings
                    {
                        ResetCustomerManagerDataOnVersionChange = false,
                        ResetPaymentManagerDataOnVersionChange = false,
                        ResetExtendedManagerDataOnVersionChange = false,
                        ResetShippingManagerDataOnVersionChange = false,
                        ResetOfferManagerDataOnVersionChange = false,
                        EmptyBasketOnPaymentSuccess = false,
                        ApplyTaxesToInvoice = true,
                        RaiseCustomerEvents = false
                    });

This issue seems to have been introduced between 2.2.0 and 2.5.0 as it is not currently happening on the production site. Any ideas on how to work around it would be appreciated.

Thanks, Simon

So, in CheckoutExtensions.cs there is an internal method called CreateCheckoutContext, at the point of entering this method my IBasketObject contains an item, the item I see in my cart.

After the call to basket.Validate() the basket then has no items! Progress? Perhaps, but no closer to finding the source of the issue at the moment still but will start look into the possibility of some failed basket validation at the moment being the cause.

Is this to do with the basket strategy in the merchello.config?

<strategy alias="DefaultAnonymousBasketConversionStrategy" type="Merchello.Web.Workflow.BasketConversionByDiscardingPreviousCustomerBasket, Merchello.Web" />
    <!--strategy alias="DefaultAnonymousBasketConversionStrategy" type="Merchello.Web.Workflow.BasketConversionByCombiningAnonymousBasket, Merchello.Web" /-->

By default, BasketConversionByDiscardingPreviousCustomerBasket is by default... maybe you need the other strategy. Just uncomment it and comment out the one above.

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