Apply tape either side apply , even smooth off .. Then carefully pull up tape .. Silicon is a pita to paint ! Try using another sealer ? Such as sicoflex ? Or similar .
I have found in the past that it is a better long term proposition to attack any leaks before they get to the inside "skin". Depending on the window type You should be able to remove the complete unit via a series of screws on an outer flange, once the window & frame is removed .Thoroughly clean both contact surfaces, apply a sealer tape to the van surface & reset the window frame.
This way You are keeping the water outside where it cannot damage to the internals of cavaties etc. The sealer tape is available from Camec and similar.