[Fizzlemizz]

When you call ADDON.SpellRow:CreateRow(parent, index, spell) the self inside that function refers to the ADDON.SpellRow table. You're saving each new row as ADDON.SpellRow.frame and overwriting the previous reference. Then funtion returns ADDON.SpellRow (self).

ie.
row[1] will = ADDON.SpellRow
row[2] will = ADDON.SpellRow
row[3] will = ADDON.SpellRow
...

and ADDON.SpellRow.frame will always contain the last row created.

The functions should look a bit more like the following so they can identify which row they should act on.

function ADDON.SpellRow:CreateRow(parent, index, spell)
  -- create a distinct new local reference to a new frame each time   
    local frame = CreateFrame('BUTTON', 'spellIdRow' .. index, parent)
    frame:SetSize(ADDON:Scale(290), ADDON:Scale(16))
 
    frame.background = frame:CreateTexture(nil, 'BACKGROUND')
    frame.background:SetAllPoints(frame)
    frame.background:SetTexture([[Interface\AddOns\AstralAnalytics\Media\Texture\Flat.tga]])
    frame.background:SetAlpha(.6)
    frame.background:Show()
 
    frame.name = frame:CreateFontString(nil, 'OVERLAY', 'GameFontNormal')
    frame.name:SetPoint('LEFT', frame, 'LEFT', 4, -1)
    frame.name:SetTextColor(1, 1, 1)
    ADDON.SpellRow:SetSpell(frame, spell)
    return frame
end
 
function ADDON.SpellRow:SetSpell(self, spell)
    local name, rank, icon = GetSpellInfo(spell)
    self.name:SetText(name .. " (" .. spell .. ")")
    self:Show()
end
 
function ADDON.SpellRow:ClearSpell(self)
    self.name:SetText('')
    self:Hide()
end
 
local function CreateSpellList()
    for key, value in pairs(row) do
        ADDON.Print("Hiding")
        ADDON.SpellRow:ClearSpell(value)
    end
 
    row[1] = ADDON.SpellRow:CreateRow(listScrollFrame, 1, 1)
    row[1]:SetPoint('TOPLEFT', parentListContainer, 'TOPLEFT', 25, -10)
    local currentRow = 1
    for spellId, _ in pairs(AstralAnalytics.spellIds[currentDropdownValue]) do
        if row[currentRow] == nil then
            ADDON.Print('new row for ' .. currentRow .. ' with id ' .. spellId)
            row[currentRow] = ADDON.SpellRow:CreateRow(listScrollFrame, currentRow, spellId)
            row[currentRow]:SetPoint('TOPLEFT', 'spellIdRow' .. currentRow-1, 'BOTTOMLEFT', 0, 0)
        else 
            print('setting existing row for ' .. currentRow .. ' with id ' .. spellId)
            ADDON.SpellRow:SetSpell(row[currentRow], spellId)
            row[currentRow]:Show()
        end
        currentRow = currentRow + 1
    end
    ADDON.Print(table.getn(row))
end

I didn't change all the code because the CreateSpellList() shouldn't work this way (continually replacing the entries in row[] and losing the old ones) so this is not really a fix, just an explanation as to why you weren't seeing the rows refresh as you expected.