Yes, it will be wrong. This still happens to me, too. I thought Bob had fixed this in one of the version 5 hotfixes, but it doesn't work right for me now in version 6 either. I typically take a "default filter" exposure at the end of the night so that the focuser is repositioned to the default focus position and the filter itself is moved to the default filter position. It could be, I think, scripted as part of the Terminate() process when ACP shuts down.
Hmm... OK, I'll have to fix this one for 6.0. I can't see an old/closed issue in the tracker for this, so here's a new one for 6.0.

http://gemini.dc3.com:8472/Gemini/De...spx?p=17&i=532