Using xverbs

inkscape --xverbs=xverbs.yaml

Format of xverbs.yaml

verbose: yes # only "verbose: yes" enable logging
run:

 # open document to process
 - xverb-id: XFileOpen, gfx_sources/loading_screen/sandclock_atlas.svg

 # set label for XUndoToLabel xverb works
 # NB: if something wrong with undo labels use verb EditUndo instead of XUndoLabel and XUndoToLabel at all
 - xverb-id: XUndoLabel, fresh_document

 # select element to handle
 - xverb-id: XSelectElement, top_sand

 # verbs
 - verb-id: EditInvertInAllLayers
 - verb-id: EditDelete
 - verb-id: FitCanvasToDrawing

 # save element to separated svg document
 - xverb-id: XFileSaveAs, output/thegame/linux/data/gfx/loading_screen/top_sand.svg

 # also save png preview
 - xverb-id: XFileExportPNG, output/thegame/linux/data/gfx_preview/loading_screen/top_sand.png

 # return to the fresh_state of document
 - xverb-id: XUndoToLabel, fresh_document

 # do any other handling
 # Inkscape have a lot of useful verbs
 - verb-id: FileQuit