There's an easy way to get some missed stuff to count towards chapter summary. As an example I use two essences I have stored - Fifth Element and Tainted Essence. If you don't have them you can use different ones by finding items ID in artifacts.cfg. By placing specific items from the storage to your inventory you will unlock desired content. We will be editing Questlist_techquest.cfg in Quests folder. Just add the new lines at the end.

If you offered Woody a hat but want to get hidden content:

missed_stuff
{
Chapter=0
Stage0
{
State=Inactive
OnItemGot:tainted_essence
{
AddStoryData=dinner_for_ghoul
}
}
}

If you want to get chimera hidden content without spawning the pile of shit:

missed_stuff
{
Chapter=0
Stage0
{
State=Inactive
OnItemGot:tainted_essence
{
AddStoryData=chimera_kaki
}
}
}

If you finished "Caverns of Steel" mission in chapter 5 and unlocked secret area but want to get hidden content in chapter 6 (here we have to remove story data first then add it again using different item):

missed_stuff
{
Chapter=0
Stage0
{
State=Inactive
OnItemGot:fifth_element
{
RemoveStoryData=td5_secret
}
                OnItemGot:tainted_essence
{
AddStoryData=td5_secret
}
}
}

As for the quests, to remove them from the count simply find the quest you missed in files from Quests folder and change the line Chapter=[number] to Chapter=0.