You should be able to reset the Group (and brace) on the two-stave systems manually.

I notice your two-stave systems have overlapping treble and bass clefs (and key signatures) on the bottom staff. How are you achieving this change from three- to two-stave systems?

If I understand you correctly, you need 3 staves in all systems, right? (so that neither staff nor bracket disappears)

… it changes from 3 staff to 2 staff …

That is not what I see in the attached graphic.

I see 3 staves in all systems, but in System 2 and System 4 I see overlapping staves.

Things to try:

(Staff Tool)

1) Switch to Scroll View.

Are the staves in Scroll View spaced as needed?

If not, respace them.

You can use

Staff menu > Respace Staves…

or space the staves individually, e. g. via

Staff menu > Staff Usage…

2) Switch to Page View.

Staff menu > Respace Staves…

Choose the option {Set to Scroll View Spacing}.