Generally, during and after a merger, there is a lot of instability in a company as layoffs in comparable departments get figured out and company infrastructures get merged. I assume that on the software side, you were insulated from this instability since they were going to need to keep developing Quartus (or its replacement) either way and Intel had no equivalent.
I was an Altera customer before and during the merger (including after it was announced). It looked from the outside like sales teams and chip design teams had significant amounts of instability. I personally experienced months of delays getting Arria 10s (and associated FAE support) from our sales team immediately after the acquisition. Our new sales team from Intel (figured out 8 months later) was twice the size, had to push CPUs and Intel's software in addition to FPGAs, and was also dealing with the embarrassing situation around Stratix 10 delays.