I want to be able to run the 'split with lines' function, but only on polygons where the area > determined value.
Is it possible to do this simply, ie running a process from the processing toolbox only when a condition is met in QGIS?
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Yes, if you look at the tool parameter you'll see that there is a tick box for 'selected feature only'
All you have to do is to select the polygon you want to split (manually, with the 'select by expression' button or by using the processing tool 'select by expression') on your polygon layer then run the 'split by line' tool with the box checked.
Note that you could also select the line to be used for splitting in the same way.