I had a similar issue with CT 36 Autoclean on this weekend. The symptoms were:
1. The suction was consistently low
2. The dust extractor would periodically shut down on its own. They tool would continue running, though. A strange feeling that you hear that the noise changed, but you do not know why.
3. Forced autocleaning, with closed blast gate, would help a little, but for only a very short time, and suction was still too low.
I noticed that early in the day, but could not readily figure out what was wrong. I thought maybe airways were clogged, either in the vacuum hose or in the tool. Checked everything, did not find any problems. I could not imagine that autoclean function could not clean the filter, with bag half empty, and did not want to mess with opening the vacuum and checking the filter inside of the house.
After I was done for the day (with unusual amount of dust around), I took the CT 36 AC outside for cleaning. It turned out that dust accumulated and got compressed into fairly hard "dust sheets" between the folds of the 1 micron filter. Since they were squished within the filter, the AC function was unable to shake them off, and the filter was heavily clogged. This explains both the low suction and overheating of the motor of the dust extractor which led to protective shutdowns.
The possible reason for this clogging was that the day before I was running CT 36 until the bag (plastic liner for drywall dust) was totally full, all the way to the filter. There was no room left to shake off the debris. Maybe this is when dust got compressed. I replaced the bag (meaning, plastic liner), but did not check the filter. The other possibility is that one might need to check the filter and clean it as necessary each time when the bag is replaced.
The solution was to take the 1 micron filter out of its plastic holder (the one with the locking handle, refer to the instructions on replacing the filter). It is relatively soft and pliable and can be bent like an accordion. Once you bend it, all folds in the filter open up. This enables one to easily clean up the debris with a finger, if they do not fall out on their own. Took a minute a less to do. After that, the suction was fully restored. The filter is made of fairly heavy duty cloth (or what appears to be a cloth), not paper, so there is no risk of damaging it.
Before I did that, I tried vacuuming the filter, but this did not work.