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Technicalfool: Sorry this took a while for a response. For now, you can still select the old decouplers in the VAB by going to the Advanced tab, selecting "filter by module", and clicking the "decouplers" type-button.
Any ideas for me? I have basically the same mission, but upgraded KSP while en route. So my issue is not trying to build with the obsoleted part, but trying to complete the mission having built with it.

I was supposed to land on Eve with the TR-18D. (on my third try) I did. But the usual contextual menu for the part "run test" doesn't appear. I have two green check marks for the objectives: Eve, Landed. And if I stage the vehicle, the separator activates, but the mission doesn't change/complete.
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Technicalfool: Sorry this took a while for a response. For now, you can still select the old decouplers in the VAB by going to the Advanced tab, selecting "filter by module", and clicking the "decouplers" type-button.
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s_p_e_x: Any ideas for me? I have basically the same mission, but upgraded KSP while en route. So my issue is not trying to build with the obsoleted part, but trying to complete the mission having built with it.

I was supposed to land on Eve with the TR-18D. (on my third try) I did. But the usual contextual menu for the part "run test" doesn't appear. I have two green check marks for the objectives: Eve, Landed. And if I stage the vehicle, the separator activates, but the mission doesn't change/complete.
If the update broke things, there's some workarounds you can try. If you have a copy of the save files from before the upgrade, you can try downloading an older version of KSP and continuing there. There's also the alt+f12 debug menu (RShift+F12 on Linux) that you can use to force a broken (or any) contract to complete. Not perfect, but it'll get your save file back on its feet.

If you're playing completely stock, it might be an idea to report the bug on the public bugtracker, providing as much information as possible. Before-and-after zips of the save directories would be ideal. It's not a guarantee of a specific fix, but it may help with future updates.