Her spirits still continued very high, but there was a flutter in them …and this agitation increased …She could scarcely eat any dinner, and …seemed anxiously listening to the sound of every carriage. (Ch. 26)

I agree Col Brandon did think of Eliza (his lover) when he saw Marianne’s state (above) in Ch. 26. In chapters 11 and 31 he compares Marianne’s mind to Eliza’s:

I once knew a lady who in temper and mind greatly resembled your sister, who thought and judged like her, but who from an enforced change -- from a series of unfortunate circumstances… (Ch. 11)

"I alluded to a lady I had once known, as resembling, in some measure, your sister Marianne. …If I am not deceived …there is a very strong resemblance between them, as well in mind as person -- the same warmth of heart, the same eagerness of fancy and spirits. (Ch. 31)

Perhaps Brandon asks “Is your sister ill?” because he was shocked to see Marianne so agitated with grief and disappointment at seeing him rather than Willoughby. He might have immediately compared Marianne to Eliza and her disappointments which eventually led to the formers disillusionment and death:

So altered -- so faded -- worn down by acute suffering of every kind! hardly could I believe the melancholy and sickly figure before me, to be the remains of the lovely, blooming, healthful girl, on whom I had once doated. (Ch. 31)

I think Brandon’s visiting “almost every day; to look at Marianne and talk to Elinor” (Ch. 27) gave him a ringside seat to what he most feared—to see Marianne’s spirit and health deteriorate from unrelenting anxiety and disappointment:

“her mind was never quiet; the expectation of seeing him every hour of the day, made her unfit for anything” (Ch. 27); “unwilling to dance …and never so much fatigued by the exercise” and “too restless for employment, too anxious for conversation, walked from one window to the other, or sat down by the fire in melancholy meditation” (Ch. 27); “wholly dispirited, careless of her appearance, and seeming equally indifferent” and “She sat by the drawing room fire after tea, …without once stirring from her seat, or altering her attitude, lost in her own thoughts and insensible of her sister's presence” (Ch. 28)

Compare dear Col Brandon’s reaction to Marianne’s distress to Willoughby’s in Ch. 15:

They were no sooner in the passage than Marianne came hastily out of the parlour apparently in violent affliction, with her handkerchief at her eyes; and without noticing them ran up stairs….

"Is anything the matter with her?" cried Mrs. Dashwood as she entered -- "is she ill?"

"I hope not," he replied, trying to look cheerful; and with a forced smile, presently added, "It is I who may rather expect to be ill -- for I am now suffering under a very heavy disappointment!" (Ch. 15)