For update, always use “Template Only” folder from your ThemeForest package, never Quickstart. If you want to update (install) “Template Only”, do it via Joomla’s installer: administrator > Extensions > Manage > Install > Upload > flex_3.9.8_template_only.zip (for Flex 3.9.8 version).

Extensions: SP Page Builder, SP Simple Portfolio, Virtuemart and AP Smart LayerSlider – all extensions except Acymailing, should be updated via Joomla’s installer: administrator > Extensions > Manage > Install > Upload > extension.zip.

All extensions are located in “Extensions” folder of your downloaded package from Themeforest.