Undefined index, variable notices

Today the following notices started to appear after working on my theme.

Notice: Undefined index: highlighted in include() (line 124 of page.tpl.php).
Notice: Undefined index: sidebar_first in include() (line 136 of page.tpl.php).
Notice: Undefined index: sidebar_second in include() (line 142 of page.tpl.php).
Notice: Undefined variable: doctype in include() (line 1 of html.tpl.php).
Notice: Undefined variable: rdf in include() (line 2 of html.tpl.php).
Notice: Trying to get property of non-object in include() (line 2 of html.tpl.php).
Notice: Undefined variable: rdf in include() (line 2 of html.tpl.php).
Notice: Trying to get property of non-object in include() (line 2 of E:\web_folders\sites\agd.sa.gov.au\www\sites\agd.sa.gov.au\themes\omega\omega\templates\html.tpl.php).
Notice: Undefined variable: rdf in include() (line 3 of E:\web_folders\sites\agd.sa.gov.au\www\sites\agd.sa.gov.au\themes\omega\omega\templates\html.tpl.php).
Notice: Trying to get property of non-object in include() (line 3 of html.tpl.php).

I did not implement major changes, but maybe I caused cache to refresh, bringing out some issues that may have been there before?

I did some searching and it seems that changes to regions may have something to do with this. I removed the sidebar regions from my subtheme weeks ago but that never caused major issues...

Does anyone know how to tackle this? Much appreciated!