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In the current 1.13.2+ versions of the mod only placements created for *.litematic files have persistent placements. If you directly load a '.schematic file, those placements will vanish when you leave the dimension.

For now you can use the Schematic Manager menu to Import and save the schematic in the Litematica format, and then use that version, and you will have persistent placements.

I already rewrote how the schematic stuff is handled in the main development code a year ago. All schematic formats are handled more or less equally and thus they all also have persistent placements in that new code. That code is currently only in the 1.12.2 LiteLoader releases.