Pairwise alignment can break the collapsing mode consistency

Scenario to reproduce:

1. Open "_common_data/scenarios/msa/ma.aln".
2. Turn on the collapsing mode.
3. Expand "Conocephalus_discolor" group.
4. Open "Pairwise alignment" options panel tab.
5. Set parameters:
   First sequence: Tettigonia_viridissima
   Second sequence: Conocephalus_discolor
   Algorithm: Smith-Waterman
   Gap open penalty: 1
   In new window: unchecked
   and start the align task.
   Expected state: these two sequences are aligned, the same changes are applied to whole collapsing group.
   Current state: these two sequences are aligned, but changes are not applied to whole group, so group contains different sequences.