The interinstrumental transfer of a short-end CE method was studied. A model separation of the hexameric forms of niobium, tantalum, and their substituted ions (Nb6-xTax with 0x6) was selected as test case. The method was first optimized on a Beckman instrument and in a second step transferred to an Agilent instrument. The transfer needed updated guidelines that tackled differences in effective capillary length, 8.5 (Agilent) versus 10 cm (Beckman), because of instrumental different capillary cartridges. Differences in effective length lead to migration time and separation efficiency inequalities, illustrated by a decrease in resolution between the substituted ions. The difference in effective length was overcome by adapting the lift offset parameter of the Agilent instrument. The lift offset default setting is 4 mm and by increasing this parameter both the inlet and outlet lifts are lowered and thus the detection window can be displaced and consequently the effective length was increased. The decrease in effective length difference and the effect on the separation efficiency was investigated and led finally to a restored separation of the substituted ions. The adaptation of the lift offset parameter during short-end injection methods was added to earlier developed guidelines to facilitate interinstrumental method transfer of CE methods.