How do you deal with it?
I make sure my sensor is as clean as possible before I shoot a timelapse. Since most of the times I shoot with a high F stop to achieve maximum depth of field, if there's any dirt or dust on my sensor that results in dots on my image, especially in the sky portion where they are more clearly visible.
The dust removal tool in Lightroom works great for still images but it doesn't work for sequences. So, what do you do?
I have a couple of nice sequences I'd like to recover that are otherwise unusable due to several dust spots...

Thanx

The best option is to keep your sensor clean. Also I avoid closing the aperture too much, whenever I can.
If you have spots in a sequence it's really hard to get rid of them. I found one way that sometimes works, is use a gradient with negative clarity on the sky and avoid adding contrast to the sky with other tools, which would amplify the dirt.

I always encounter such issue but I think only way is to create the video first and then use Premier pro to get rid of the spot. I ever did removing the spot on LR and the result is bad as I just sync it, not removing individually. Anyway, there are dirt in the lens, which is the main culprit when our F stop is high.