If several expense claims are submitted at once then they will be part of the same header so that groups can be easily identified - eg multiple claims for one event. These take the Reference (Invoice Number) from the header.
If these are then approved and synchronised to the accounts separately, the same Reference is downloaded from Expense and if duplicate references are not allowed (to check this, click System, Options, Purchase Ledger Options) the message will be displayed. However, it is possible to change the Reference to a unique value as below:
Click Synchronise, Expenses.
Click Synchronise.
Click the Blue Ellipsis, three dots icon and select Edit.
Amend the Reference perhaps adding a _2 on the end to make the reference unique.
Click Save.
Process the expense.