Maybe email or chat with them to ask what to do? Edit the BOM to order 2x then write a note in the assembly instructions? This won’t be automated assembly anyway.
Here is the problem source. If you have two separate elements it is better to have a separate footprint for each of them. It needs more care to position them in right distance but not generates a problem with quantity.
The other solution is (I have never used JLCPCB) to have for such symbol/footprint a description in BOM beginning with 2x… . To tell you the truth I have never used this 2x but I used descriptions like 1/5 of … when some pin header (with custom pin length) had to be ordered in minimum 1000 pcs and we agreed with contract manufacturer that he orders 10 pin headers and cuts it into needed 5 pin and 2 pin parts.
One solution is to make a schematic symbol for half a fuse, and then put two of them in the schematic, and then hide the Reference and value fields for the “other half” of the fuse.
KiCad does not have support for sub assemblies (yet). Even if you use two half fuses, then you still only have the clamps, it still does not include the fuse itself. Similar for socketed IC’s, parts that need fasteners, etc.