Why is my for loop only half-working? (R) - r

Question

I'm not sure how to make a reproducible example of my problem and this post is very verbose. I was hoping the issue might pop out. Basically, this for loop obtains output from an external program, makes some calculations in R, and then posts the results of those calculations back into an external file.
The first iteration of the loop runs perfectly fine. It does everything correctly then proceeds to return to the top of the loop and change to the correct directory (flist[2]), but when it reaches the second function (get_stress_table), it chokes by printing "NAs" into the files rather than the file names (flist, which is a vector of file names).
The file names and sub directories being iterated through in this loop share a common name. The fact that it correctly changes to the right sub-directory in setwd, but prints 'NA' as a file name in the first function is what confuses me. Thus I don't understand the problem.
Anything sticking out?
Here is the for loop I am trying to run:
for (i in 1:length(flist)){
setwd(paste0(solutions_dir, "\\", flist[i]))
max_stress <- get_stress_table(solutions_dir = solutions_dir, flist = flist[i], lsdynadir = lsdynadir, states = 5)
xy_table <- element_time_series(stressed_eid = max_stress, solutions_dir = solutions_dir, flist = flist[i], lsdynadir = lsdynadir)
damp_coeff <- find_damp(xy_table = file_xy)
setwd(kfile_complete)
erode_damp(erosion_lines = erosion_lines, damp_coef = damp_coeff, kfile_mesh = flist[i])
}
Here is the error I return:
3.
file(con, "r")
2.
readLines(flist[i])
1.
get_stress_table(solutions_dir = solutions_dir, flist = flist[i],
lsdynadir = lsdynadir, states = 5)
Here is the inside of that function:
biggest_stresses <- data.frame(eid= numeric(),
stress = numeric(),
stringsAsFactors=FALSE)
for (j in 1:states) {
fileconn <- file("get_stresses.cfile")
line_one <- paste0("open d3plot ", solutions_dir, "\\", flist[i], "\\", "d3plot")
line_two <- "ac"
line_three <- "fringe 14"
line_four <- "pfringe"
line_five <- "anim forward"
line_six <- "anim stop; state 100;"
line_seven <- paste0("output ", solutions_dir, "\\", flist[i], "\\", flist[i], " ", j, " 1 1 1 0 0 0 0 1 0 0 0 0 0 0 1.000000")
writeLines(c(line_one, line_two, line_three, line_four, line_five, line_six, line_seven), fileconn)
close(fileconn)
system(paste0(lsdynadir,"\\lsprepost4.3_x64.exe c=get_stresses.cfile -nographics"))
stresses <- readLines(flist[i])
start <- grep(stresses, pattern="*KEYWORD",fixed = T)
stop <- grep(stresses, pattern="$Interpreted from averaged nodal data",fixed = T)
stresses <- stresses[-seq(start, stop, by = 1)]
writeLines(stresses, flist[i])
stresses <- read.table(flist[i], header = FALSE)
names(stresses) <- c("eid", "stress")
max_stress <- which(stresses$eid == which.max(stresses$stress)
biggest_stresses <- rbind(biggest_stresses, stresses[max_stress,]
}
return(biggest_stresses[which.max(biggest_stresses$stress),1])
}