The other answers haven't addressed putting this into one (property changing) loop, and though in this situation it's perhaps not the best solution, it can be done.

Joining Two Lists

We have two lists:

local walls = game.Workspace.InvisibleWalls:GetChildren()
local doors = game.Workspace.Doors:GetChildren()

We can join them together to make a single list (though this requires a loop since Lua does not have this as a built in function)

local parts = walls
for _, door in pairs(doors) do
    table.insert(parts, door)
end

We can now have a single loop that will change the properties of objects in both lists (because we've turned it into just one)

We want all parts to have their CanCollide property set to false, and just those children of Doors to become invisible. It could look like this:

for _, part in pairs(parts) do
    if part:IsA("BasePart") then
        -- If `part` is actually a Part as opposed to some other
        -- object like a Script or Model
        part.CanCollide = false
        if part.Parent == workspace.Doors then
            -- Is a door
            part.Transparency = 1
        end
    end
end

Or, Using a New Iterator

We can define our own ipairs like iterator for a for loop which will take two lists in and just iterate over both of them. This means we no longer need the initial joining loop, though we do need a more complicated construct..

function joinobjs(one, two)
    local i = 0
    return function()
        i = i + 1
        if i <= #one then
            return one[i]
        elseif i <= #one + #two then
            return two[i - #one]
        end
    end
end

Now we just use the loop from the previous one with a different line for the for:

for part in joinobjs(parts) do
    if part:IsA("BasePart") then
        -- If `part` is actually a Part as opposed to some other
        -- object like a Script or Model
        part.CanCollide = false
        if part.Parent == workspace.Doors then
            -- Is a door
            part.Transparency = 1
        end
    end
end

As you may know, GetChildren returns a table of every child of the parent. In order to set all of the children individually you must iterate through the table.

Two Options

Option 1

local children=Workspace.InvisibleWalls:GetChildren()
for i=1, #children do
if children[i]:IsA("BasePart") then --make sure we are editing a part!
children[i].CanCollide=false
end
end

Option 2

local children=Workspace.InvisibleWalls:GetChildren()
for index, value in pairs(children) do
if value:IsA("BasePart") then --make sure we are editing a part!
value.CanCollide=false
end
end

As promised:

for _, v in ipairs(Workspace.InvisibleWalls:GetChildren()) do
    if v:IsA("BasePart") then
        v.CanCollide = false
    end
end

This, I should mention, is functionally identical to l0cky's "Option 2", just using current practices.