rules state the following: Runs use the Real Time Attack (RTA) timing convention, which means it measures the real time that has passed from start to finish, rather than in-game time. Runs may be timed with an external timer (such as WSplit), though the timer does not have to be shown on video.

So, sadly no you cannot stop the timer and resume it upon your return and not have the time you was away not to count.

thats called segmented run. I suggested already but only if like 15+h