It looks like there is a continuing issue causing the acetylene formation. A plan for repair should be undertaken as soon as possible. The H2 appears to be increasing also, only very slowly, but H2 production can come from other things. The nature of the problem is likely small and high energy...
The process does play a role in the removal of gasses. My experience with vacuum refills has been that there is always a shadow of the original left over. It can take some time for the levels to reach a new equilibrium and some may not reach the detection threshold until a problem occurs. OP's...
The acetylene level is still pretty low, but the trend is increasing and the elapsed time should be long enough for it to have diffused out of the paper. I would think about a plan though not take any action until the level is a little higher. Definitely increase the frequency of the DGA tests...
It will take time for the gasses to exchange out of the paper. Have there been any tap changer operations since re-energization? Arcing in the tap changer may be a problem also. Could you post the results of the recent DGA and that of before it was returned to service?
Yes, the gasses are in all of the oil after a time and the oil is held in the paper for a long period even after it is drained. The gasses trapped in the paper will eventually reach an equilibrium with the rest of the oil if no problems are present. When the transformer is refilled under vacuum...