I have Houdini Indie 16.5.345, several weeks ago I used one of free asstets from Orbolt (free but when downloading it was described as commercial). Today I wanted to update my asset used in UE4 project and after reimporting and recooking it crashes with error:

Houdini License issue - (HoudiniAssetActor_1) : (Finished Instantiation with Errors: HAPI Error: Limited commercial (Indie) assets not allowed with commercial licenses.).

Is it known issue?

That error happens when houdini has acquired a commercial license and tries to load an Indie hda (.hdalc), which is not supported. If you are have Indie license installed and this happens with the ue4 plugin, please log a bug with your license manager diagnostic info attached because it should work.