I can't find a conclusive answer, but here's what I did find:

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The script is no help - it doesn't even mention the conversation between the Russians before Floyd approaches them, and all it says about their conversation after he leaves is:

THE RUSSIANS EXCHANGE A FEW SERIOUS PARAGRAPHS IN RUSSIAN

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From the comments on the YouTube video itself:

LEFTCOASTER67: Does anyone know how good the actors [sic] Russian is?

ECONOMIC: To a Russian speaker, it is obvious that he (Rossiter) is not Russian or even eastern European. Having said that, he does pronounce the phrases with correct emphasis, albeit with an overtly English tongue ;)

INGUSMANT: What does he say at the end btw?

ECONOMIC: Not too sure I am interpreting it correctly but it sounds like "Navernoe im ochen trudna" which roughly translates as 'It looks like it's difficult for them' or 'It looks like they're struggling'. The woman then replies and that roughly translates as 'it seems like it'.

And:

DEEPTIME5: What are they saying in Russian at the end of the clip..? I've always wondered.

SUISEISEKI DESU: "I guess it must be difficult for them." "Apparently."

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From a scholarly analysis of film effects:

After Dr. Floyd leaves, Dr. Smyslov speaks ill of him. “Наверное, ему очень трудно./Definetly, he has the greatest difficulty.” Dr. Stretyneva responds, “По видимости./Obviously.” Dr. Kalinan does, too, “Да, очень трудно./Yes, the greatest difficulty”.

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From IMDb:

Before they meet Floyd, they are considering going to the observation deck while they wait for a flight. After Floyd leaves, they say, "It must be difficult for him."

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From the FAQ on a Kubrick fan site:

What does the Russian scientist Smyslov say on the space station in 2001?

[A site member named] Dupavoy answered this one, he translates it as: "These are hard times."

Although, according to Nina Stoessinger, in the German dubbed version Smyslov says: "He knows more"

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From a sci-fi fan site:

"Im navernoe ochen' trudno" ("They must have had a very hard time").

"Da, ochen' trudno" ("Yes, they must").

Which suggests the subject of the Russians' concern had less to do with Floyd than with the crew of the Russian rocket bus.

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This last translation seems to be based on an earlier post on an extensive 2001: A Space Odyssey fan site:

The female scientist remarks: "Im navernoe ochen' trudno" ("They must have had a very hard time").

Margaret Tyzack replies: "Da, ochen' trudno" ("Yes, they must").

It suggests that the subject of their concern was nothing to do with Floyd, but was the crew of the Russian craft that was denied permission for an emergency landing.

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My take on the above:

A YouTube user who speaks Russian well enough to critique Rossiter's enunciation has interpreted it on his or her own, and says it is something like:

'It looks like it's difficult for them' or 'It looks like they're struggling'... 'It seems like it'.

Another YouTube user has a different translation with the same basic meaning:

"I guess it must be difficult for them." "Apparently."

While several other sources (which may be dependent upon one another) say the lines are:

"They must have had a very hard time".

"Yes, they must".

Thus, we have at least three (seemingly) independent translations that say roughly the same thing. Chances are, they are correct.

This conclusion is supported by the fact that at least one other source translates the first line as "These are hard times", which is quite similar to "They must have had a hard time". Most of the translations agree that the first line has something to do with hard times.