I can't see where the problem is without a reprex (see the FAQ. A data.table object can be written to disk with SQLLITE() and, if read back in and converted to a data.table object it will be identical to the original object, as shown
library(data.table)
library(RSQLite)
set.seed(42)
(d <- data.table(o = c(NA,1:9)))
#> o
#> 1: NA
#> 2: 1
#> 3: 2
#> 4: 3
#> 5: 4
#> 6: 5
#> 7: 6
#> 8: 7
#> 9: 8
#> 10: 9
con <- dbConnect(RSQLite::SQLite(), "dat")
dbWriteTable(con, "d", d)
dbListTables(con)
#> [1] "d"
(d2 <- dbGetQuery(con, "SELECT * FROM d"))
#> o
#> 1 NA
#> 2 1
#> 3 2
#> 4 3
#> 5 4
#> 6 5
#> 7 6
#> 8 7
#> 9 8
#> 10 9
dbDisconnect(con)
con <- dbConnect(RSQLite::SQLite(), "dat")
dbListTables(con)
#> [1] "d"
(d2 <- dbGetQuery(con, "SELECT * FROM d"))
#> o
#> 1 NA
#> 2 1
#> 3 2
#> 4 3
#> 5 4
#> 6 5
#> 7 6
#> 8 7
#> 9 8
#> 10 9
dbDisconnect(con)
identical(d,d2)
#> [1] FALSE
# because
class(d)
#> [1] "data.table" "data.frame"
class(d2)
#> [1] "data.frame"
# so
d2 <- data.table(d)
identical(d,d2)
#> [1] TRUE
Created on 2023-04-06 with reprex v2.0.2