You could create the timer in the OpeningFcn:
handles.save_timer = timer( ...
'ExecutionMode','fixedRate', ...
'Period',1800, ... % 30 min = 1800 s
'TimerFcn',{@cb_save_table,handles.figure1}); % <- pass the figure to the TimerFcn
Start the timer when the process that takes > 5-6 hours starts (that might be when the GUI starts (OpeningFcn) or it might be in a Callback in the GUI):
start(handles.save_timer);
And define the TimerFcn of the timer to be the callback you posted, which saves the table data to file:
function cb_save_table(src,evt,fig)
handles = guidata(fig);
writetable( ...
cell2table(get(handles.uitable1, 'data')), ...
sprintf('%s.csv', datestr(now, 'dd.mm.yyyy.HHMM')));
end
