She has repressed feelings, demonstrated both in the comic strip, where she did like him at the start, and is shown to care about him throughout the years in moments spread throughout the series.
In the specials, prior to "You're in Love" Lucy had been shown to really care about whether or not Charlie Brown thought she was pretty, as found in the Christmas Special. Beyond just being an expression of vanity though, its repeated in this very special, where Lucy once again becomes agitated and taken aback over Charlie Brown not finding her pretty (https://www.dailymotion.com/video/x4jws81
9:40) . Beyond a simple demonstration of Lucy's vanity though, this general sentiment between Lucy and Charlie Brown is echoed in the Psychiatric Booth skit for this particular special (13:20). After yet another unsuccessful endeavor with Schroeder, Lucy tends to her psychiatric booth, presumably to take her anger out on someone else. Her natural crabbiness is amplified as Charlie Brown describes that he's there because of , which sends Lucy into a rant about her own love troubles, with a particular remark about how "you men are all alike."
So why did Lucy write the note? The date gag (15:40) satirizes this idea of the duo's love troubles and through making the joke connects their struggles to each other. The kicker though is the little visual gag seen as Charlie works through a math problem in order to impress the TLRHG (23:02/pic related). For those unaware, its referencing the phrase "A fine line between hate and love." It's a very peculiar joke to make, and being right before the final scene where Charlie Brown receives the note, it comes off as more of a hint than as a background joke, considering its relevance to the theme of the special as well.
Lucy is shown to sometimes show sympathy for Charlie, and I believe after their shared experience last night, and knowing that Charlie has a crush on TLRHG, chose this way to express her repressed feelings for him(cont.)