Those flights were mainly operated by Lufthansa partner airlines with 30-50 seaters (Contact Air, Augsburg, Cirrus). Those partner airlines no longer exist and Lufthansa has no suitable own equipment in the right places. The only aircraft left in the Lufthansa fleet useful for LCY ops are the E190s of Lufthansa Cityline. These are based in Frankfurt for hub feed (and operate the LCY route from there). Eurowings, which used to man the bases at places like HAM and DUS only has unsuitable CR9s, Munich no longer has Citlyine RJ85s but only E95s and CR9s etc. etc.
Additionally, Lufthansa seems to have decided that they will concentrate on LHR: There were times when they had a sizeable network out of STN, later they built up a presence at LCY. For the time being, it is all LHR.