graphic made of dots: how to transform each when partially grouped.

If you ungroup object and effects disappeared, that can mean that user apply effect to group. That mean that user created it via Transform Effect? Do you have any Effects in your appearance panel?

It would indeed be useful if you can provide a sample Illustrator file for inspection.

Apart from that, some notes based on what you described so far: If you have a group of filled objects that lose their fill attributes as soon as you ungroup them, this most likely indicates that the fill attributes were applied at the group level using Add New Fill in the Appearance palette. This is probably what you have, but you may clarify it by sharing a sample file.

As for the Transform Each command: It usually does not work with single groups as you may expect, that is, it doesn't transform each object within the group. As you already noticed, it treats the entire group instead. Normally, ungrouping the group is sufficient to get the desired Transform Each behaviour, but there can be various reasons why one doesn't want to ungroup things.

Talking about simple groups (not nested) that contain path objects, there is a way to apply Transform Each without having to ungroup first. Just select the group, take the Direct Selection tool and Shift click on one arbitrary anchorpoint to deselect just this point. After that, Transform Each should work as if the grouped objects were ungrouped.

If you have nested groups, it is a bit more complicated to use this trick because it strictly works at a per single group level. That means that you then have to deselect multiple anchorpoints to get Transform Each right.

You may now protest and claim that it would be much easier to select the group, enter Isolation Mode and perform Transform Each as it looks like Isolation Mode temporarily ungroups groups. Unfortunately, this would be a wrong conclusion because Transform Each in Isolation Mode still treats the whole group and not its child objects.

If all that doesn't make sense in your case, you may want to provide a sample file.

Damian,

"I believe my predecessor grouped parts of it"

If that is the case, I believe you can expand the relevant Layer(s) in the Layers panel, then further expand any Group(s), then, just working in the Layers panel:

1) For the/each Group, ShiftClick all the dots to select them, then ShiftClick one dot to unselect it, then apply Transform Each to the others, then select the last one and apply Transform Each, then lock the Group;
2) Select everything and apply Transform Each (which will transform all the Ungrouped ones;

3) Unlock the Groups.

This could be easier/less painful than dealing with the unknown.

It would be best if you could upload a demo  file to check out (Dropbox or the like)