Not sure if it's user error so i'll refrain from assigning a label to avoid clutter.
The above behavior was independent of previewer (zathura/sioyek). On consequent uses, the previewer doesn't autosload but if opened and navigated to the file manually, it works. It seems that pandoc is executing normally. Pic related. It also seems knap.close_viewer doesn't work.
For debugging purposes i used the following stock config (found the readme). It is supplied below. The file is located under ~/.config/nvim/after/plugin/knap.lua (and thus is lazyloaded)
-- set shorter name for keymap function
local kmap = vim.keymap.set
-- F5 processes the document once, and refreshes the view
kmap('i','<F5>', function() require("knap").process_once() end)
kmap('v','<F5>', function() require("knap").process_once() end)
kmap('n','<F5>', function() require("knap").process_once() end)
-- F6 closes the viewer application, and allows settings to be reset
kmap('i','<F6>', function() require("knap").close_viewer() end)
kmap('v','<F6>', function() require("knap").close_viewer() end)
kmap('n','<F6>', function() require("knap").close_viewer() end)
-- F7 toggles the auto-processing on and off
kmap('i','<F7>', function() require("knap").toggle_autopreviewing() end)
kmap('v','<F7>', function() require("knap").toggle_autopreviewing() end)
kmap('n','<F7>', function() require("knap").toggle_autopreviewing() end)
-- F8 invokes a SyncTeX forward search, or similar, where appropriate
kmap('i','<F8>', function() require("knap").forward_jump() end)
kmap('v','<F8>', function() require("knap").forward_jump() end)
kmap('n','<F8>', function() require("knap").forward_jump() end)
local gknapsettings = {
htmloutputext = "html",
htmltohtml = "none",
htmltohtmlviewerlaunch = "falkon %outputfile%",
htmltohtmlviewerrefresh = "none",
mdoutputext = "html",
mdtohtml = "pandoc --standalone %docroot% -o %outputfile%",
mdtohtmlviewerlaunch = "falkon %outputfile%",
mdtohtmlviewerrefresh = "none",
mdtopdf = "pandoc %docroot% -o %outputfile%",
mdtopdfviewerlaunch = "sioyek %outputfile%",
mdtopdfviewerrefresh = "none",
markdownoutputext = "html",
markdowntohtml = "pandoc --standalone %docroot% -o %outputfile%",
markdowntohtmlviewerlaunch = "falkon %outputfile%",
markdowntohtmlviewerrefresh = "none",
markdowntopdf = "pandoc %docroot% -o %outputfile%",
markdowntopdfviewerlaunch = "sioyek %outputfile%",
markdowntopdfviewerrefresh = "none",
texoutputext = "pdf",
textopdf = "pdflatex -interaction=batchmode -halt-on-error -synctex=1 %docroot%",
textopdfviewerlaunch = "sioyek --inverse-search 'nvim --headless -es --cmd \"lua require('\"'\"'knaphelper'\"'\"').relayjump('\"'\"'%servername%'\"'\"','\"'\"'%1'\"'\"',%2,%3)\"' --reuse-instance %outputfile%",
textopdfviewerrefresh = "none",
textopdfforwardjump = "sioyek --inverse-search 'nvim --headless -es --cmd \"lua require('\"'\"'knaphelper'\"'\"').relayjump('\"'\"'%servername%'\"'\"','\"'\"'%1'\"'\"',%2,%3)\"' --reuse-instance --forward-search-file %srcfile% --forward-search-line %line% %outputfile%",
textopdfshorterror = "A=%outputfile% ; LOGFILE=\"${A%.pdf}.log\" ; rubber-info \"$LOGFILE\" 2>&1 | head -n 1",
delay = 250
}
vim.g.knap_settings = gknapsettings