But I still don't see that much is gained compared to immediately interrupting the ponder, and than order a new ponder search on the same move as before. It is just a repetition of the last thing that Polyglot has done towards the engine, so it must still have all required info to do it.
I am very nervous about keeping too much state around. This makes a program unreadable/unmaintainable. Better have something that works first.
Also I have not thought about the time parameters of the ponder command. Perhaps one should just repeat them but I haven't thought about it.
BTW: I fixed one version of Toga (1.4.1SE) so that you can issue the Thread command at arbitrary times.