Dishwasher shows a drain problem - diagnosis
Since it thinks the filter is blocked, but you're not finding any blockages, I would think that the sensor that's responsible for telling the computer that nothing is flowing is failing.
A quick DuckDuckGo search for &quot;BOSCH SHEM55W55N parts list&quot; brought me to this site that has a parts diagram for the pump assembly. Scrolling through the parts list for the pump shows a sensor. Since you've been in there, make sure that's the area you're talking about, if that's not it, they have schematics for the whole machine, so you should be able to find the filter you're looking for and an associated sensor, if I've picked the wrong one.
At the current price of $30 USD, it's not the cheapest part to replace on a hunch, but it's certainly not the most expensive part, and definitely cheaper than replacing the whole thing.
No affiliation with or recommendation of the linked site - it was just one of the first options that looked good.