Small 'blistering' under surface-mount soldering attempt - is this a problem?
I'm sorry, but I can't see what you're referring to in the images.  But, if I'm understanding correctly, the "bubbling" is visible on the bottom side underneath the reworked IC "U3"?

If so, I expect the PCB itself will be fine.  The solder mask can delaminate from the substrate without breaking connections.  And even the FR4 layers can come apart a bit without trace damage.

However, I worry about U3. The bubbling shows that you got things much too hot.  You may well have damaged the IC.

I'm guessing that your purple PCBs are from OSHPark (I love OSHPark!) and were fairly inexpensive.  If I was in your situation I would simply start again on another board with a new U3.  It would solve both possible problems (the PCB or the IC) and might save a lot of time and headache.