Hey Linda,
sorry for the late reply. The temp files are only for debugging purposes from my perspective, hence the default. I'll look into it why they are being removed even if you have the option on, didn't use it for a long time (as I usually abort the lotus run if I need temp files ;) ).
Please be aware that we're planning some major LotuS updates in the coming months, so might be awhile till I patch non-critical bugs.
best,
Falk