You are doing a bunch of extra things that don't really help your cause. This:

featureData(eset)<-getNetAffx(eset, type = "transcript")

and this

eset.annot <- annotateEset(eset, annotation(eset))

do very similar things. Is there a particular rationale to do both? And then you do this:

eset1 <- annotateEset(eset.annot, pd.zebgene.1.1.st,columns = c("PROBEID","ZFIN","ENSEMBL","ALIAS","ENTREZID","SYMBOL","GENENAME"),multiVals = filter,annocols=1, probecol=2)

which is a mixture of arguments for two different methods, and probably doesn't do what you think it is doing. In the end you have three (!) different ExpressionSets that are annotated using three closely related methods. You can really only use one at a time, so having three is unnecessarily complex.

The final error comes from the fact that you are doing something that makes no sense at all, and doesn't even remotely resemble what I recommended you do. You are trying to find the Entrez Gene ID for all the genes on your array, right? But then you do this:

keys <- keys(org.Dr.eg.db)

That gets all the Entrez Gene IDs in the org.Dr.eg.db package, which corresponds to all known D. rerio Entrez Gene IDs. You then do

mapIds(org.Dr.eg.db,keys=keys,fd$SYMBOL,column="ENTREZID",keytype="ENTREZID", multiVals = list)

Which, translated to English is saying 'give me all the Entrez Gene IDs for D. rerio that are in the org.Dr.eg.db, based on this set of Entrez Gene IDs that I just extracted from that package'. The fact that you put fd$SYMBOL in that function call, without using an argument, means that it is in essence ignored.

You can use positional argument matching, where you put the arguments in the correct position, or you can use direct argument matching with the equals sign, but using a mixture of both will often have unintended consequences.

I gave you three lines of code that would have done exactly what you wanted to do, but you didn't use it! This doesn't have to be as complicated as you are making it, and you should NEVER be accessing S4 slots directly using the @ symbol! Rather than doing all this extra stuff that is not helpful, you can do what you want in very few lines of code.

This is what your script should look like:

setwd("C:\\Users\\mat149\\Desktop\\GG")
library(oligo)
CELdat <- read.celfiles(list.celfiles())
eset<-rma(CELdat)
library(affycoretools)
eset <- annotateEset(eset, annotation(eset))
## extra annotation
fd <- fData(eset)
fd$ENTREZID <- mapIds(org.Dr.eg.db, fd$SYMBOL, "ENTREZID","SYMBOL")
fData(eset) <- fd
## modeling
library(limma)
grps <- factor(rep(c("WT","lepA_MO","lepA_rescue"), c(8,4,4)))
design <- model.matrix(~ 0+grps)
colnames(design) <- gsub("grps", "", colnames(design))
fit <- lmFit(eset, design)
contrast.matrix <- makeContrasts(lepA_MO-CONTROL, lepA_RS-CONTROL, lepA_MO-lepA_RS, levels=design)
fit2 <- contrasts.fit(fit, contrast.matrix)
fit2 <- eBayes(fit2)
results <- decideTests(fit2,p.value=0.01,adjust="BH",lfc=2)

MOWT<-topTable(fit2, coef=1, adjust="BH", p.value=0.01, lfc=2, sort.by="P", n=Inf)

Note that adding in all the phenoData isn't strictly necessary, ESPECIALLY if you add it all in and then never use it for anything! Your goal should be to simplify what you do, limit extra steps, and understand what you are doing and why.