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My beam weapons (of which none is a beam; phasers are beam weapons; should have called them plasma weapons or pea shooter or something else) research state is as follow:
Efficient blasters
Long range lasers
High power blasters
Phaser intensification

In the ship designer, auto upgrading causes any shatterforce laser (which is NOT a laser) or impact assault blaster to be replaced by the pulse beam (the very first and weakest “beam weapon” available).
The design editor hides them if “Only show latest components” is checked, and lets select only pulse and maxos blasters.
I suppose the IA use pulse blasters in their design, which would explain why a 12 ships fleet threw itself at a medium space port of older design (maxos based) to be destroyed without managing to dent its shields.
I don't know what triggered this, as all seemed to work fine earlier: although pulse beam was not hidden in the designer when it should have, the shatterforce used to properly upgrade and show in the list.

What race do you play? Each race has a preference for weapons, and if you research something other than the design wants, maybe strange stuff happens?

This sounds like a bug to me. It should not be replacing third or fourth level weapons with first level weapons. The preferences mean that it may delay using a different weapon type than its preferred type until it's clearly superior, but not this. Could you upload a save file please?

Uploading right now: "Florestan pulse blaster bug.dwg"

I've got it again in another game, except this time it is with graviton beams and resonant gravitic beams. They have the same tech level, but the resonant version is considered obsolete.