Hi Gunther, first that all I wish you a Happy New Year to you and your family.
Just before Xmas I spend 3 days shooting a timelapse of the building up of a crane, the weather was terrible, heavy rain,  hence I got quit a lot of water spots on the lens, I have cleaned one photo using spot removal tool from Lightroom and then syncronized it with the remaining 3264 of  the batch, using Lightroom synchronize. Then I proceeded to export them.
Question 1 . was that the correct procedure.
Question 2 . how long does it take to complete the export?, 
it has been running for about 8 hrs and it has only done a third of the progress bar.

Kind regards,

Rodrigo

Spot removal can be added to the very first image of the sequence when editing the keyframes in Lightroom. LRTimeapse will then populate it to the whole sequence when doing the auto transition.
Another option is to synch it manually in Lightroom to all images. I prefer letting LRT do the job, because this will force the clone source to be fix.

The export from Lightroom depends on the length of your sequence, the image size, etc. It's not something related to LRTimelapse. But yes, exporting 3264 images might take a long time.
Normally I wouldn't work with such long sequences. In your case you would get nearly two minutes of film, this is much too long for anyone to watch.
Especially for long term time lapse, normally you would remove unwanted images that to not contribute to the progress that you want to show. In LRTimelapse Pro there are special filters in the long term workflow, that allow to quickly identify and remove unecessary images to make the sequence shorter. Of course this will as well save time when processing then.