Yes, they did. S10 and S12 reran in their entirety very recently with those episodes skipped, and S13 starts soon. Netflix, Hulu, iTunes, and Amazon still have the episodes. Earwig said that PBS was going to "put the Lance episodes on the shelf for a while". He didn't say which episodes, but it appears to be those three (I knew "MacGrady" and "Ride/Fiasco" would be gone, though I wasn't sure if "Binky/Operation" would since it didn't use Lance's actual likeness).
Ironically, on one of the episodes that reran within the past two weeks (I forget which), an exterior shot of the school at the start of a school scene showed "Vance Legstrong" (or someone in his signature purple shirt) riding by.