Q: Why didn't Lara Flynn Boyle play Donna in FWWM?

A: There are a few rumors...

The most probable reason is that she was involved with another project during the filming of FWWM; specifically, Wayne's World (1992):

Both Lara Flynn Boyle (Donna) and Sherilyn Fenn (Audrey) were committed to other projects at the time of FWWM production. Lynch decided to go ahead without them, rather than trying to negotiate for a later shooting date. Although it was easy to exclude Audrey's character from the script (since she had had little to do with Laura anyway), Donna's character was vital to Laura's story and so was recast with Moira Kelly.

Quote viewable here.

Another is that she didn't like some of what Donna's character was scripted to do in the movie, most likely referring to the Pink Room scenes. This contention abounds on internet movie sites such as the Internet Movie Database (IMDb): 

Lara Flynn Boyle did not reprise her TV role as Donna Hayward reportedly because of the nude scenes. She was replaced by Moira Kelly.

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This seems somewhat questionable, however, since Boyle appeared in two films around the time of FWWM's release, The Temp (1993) and The Road to Wellville (1994), in which she had several nude scenes.

Other rumors exist, founded largely on information gathered from other actors. One is that she didn't make many friends during the series (she is reportedly notorious for her "high-maintenance" personality) and didn't want to be involved any more with Twin Peaks. Another involves her by-then ended relationship with Kyle MacLachlan and her supposed unwillingness to work on a project he was part of. Yet another rumor (and one that, of these three, is probably likely) is that, like MacLachlan, Boyle was reticent to be typecast as Donna. Unlike MacLachlan, however, who simply limited his involvement with the project due to typecasting concerns, she (supposedly) steered clear of it altogether.

It should be noted here that none of these theories are 100% substantiated, and each has its own body of "evidence" to support itself. Oficially speaking, the TPG does not try to say that any of these are remotely definitive, so reader beware!

Kelly

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