It is possible to use the standard order fulfillment implementation (https://www.flexibee.eu/api/dokumentace/ref/realizace-objednavky/) by specifying the ID of the invoice being created (the orders will then be fulfilled into a single invoice).
Example
<winstrom version="1.0">
<objednavka-prijata>
<id>code:OBP0036/2019</id>
<realizaceObj type="faktura-vydana">
<id>2043</id>
<polozkyObchDokladu>
<polozka>
<cisRad>2</cisRad>
<mj>1</mj>
</polozka>
</polozkyObchDokladu>
</realizaceObj>
</objednavka-prijata>
<objednavka-prijata>
<id>code:OBP0038/2019</id>
<realizaceObj type="faktura-vydana">
<id>2043</id>
<polozkyObchDokladu>
<polozka>
<cisRad>1</cisRad>
<mj>1</mj>
</polozka>
</polozkyObchDokladu>
</realizaceObj>
</objednavka-prijata>
</winstrom>