When loading chunks that previously had command blocks in them, the command blocks will be there, however the command inside will be lost. Below I have the error log the server provides for each command block loaded.

[03:34:17] [Server thread/ERROR]: Failed to load data for block entity minecraft:command_block

com.google.gson.JsonSyntaxException: com.google.gson.stream.MalformedJsonException: Use JsonReader.setLenient(true) to accept malformed JSON at line 1 column 1 path $ at com.google.gson.internal.Streams.parse(Streams.java:60) ~[minecraft_server.18w20a.jar:?] at com.google.gson.internal.bind.TreeTypeAdapter.read(TreeTypeAdapter.java:65) ~[minecraft_server.18w20a.jar:?] at wq.a(SourceFile:493) ~[minecraft_server.18w20a.jar:?] at wq.a(SourceFile:518) ~[minecraft_server.18w20a.jar:?] at ic$a.a(SourceFile:243) ~[minecraft_server.18w20a.jar:?] at bam.b(SourceFile:69) ~[minecraft_server.18w20a.jar:?] at bmj.b(SourceFile:45) ~[minecraft_server.18w20a.jar:?] at bmf.c(SourceFile:78) [minecraft_server.18w20a.jar:?] at bqb.a(SourceFile:496) [minecraft_server.18w20a.jar:?] at bqb.a(SourceFile:101) [minecraft_server.18w20a.jar:?] at si.g(SourceFile:94) [minecraft_server.18w20a.jar:?] at si.b(SourceFile:118) [minecraft_server.18w20a.jar:?] at si.a(SourceFile:160) [minecraft_server.18w20a.jar:?] at net.minecraft.server.MinecraftServer.g_(SourceFile:384) [minecraft_server.18w20a.jar:?] at net.minecraft.server.MinecraftServer.a(SourceFile:336) [minecraft_server.18w20a.jar:?] at ru.d(SourceFile:248) [minecraft_server.18w20a.jar:?] at net.minecraft.server.MinecraftServer.run(SourceFile:497) [minecraft_server.18w20a.jar:?] at java.lang.Thread.run(Unknown Source) [?:1.8.0_171]Caused by: com.google.gson.stream.MalformedJsonException: Use JsonReader.setLenient(true) to accept malformed JSON at line 1 column 1 path $ at com.google.gson.stream.JsonReader.syntaxError(JsonReader.java:1559) ~[minecraft_server.18w20a.jar:?] at com.google.gson.stream.JsonReader.checkLenient(JsonReader.java:1401) ~[minecraft_server.18w20a.jar:?] at com.google.gson.stream.JsonReader.doPeek(JsonReader.java:593) ~[minecraft_server.18w20a.jar:?] at com.google.gson.stream.JsonReader.peek(JsonReader.java:425) ~[minecraft_server.18w20a.jar:?] at com.google.gson.internal.Streams.parse(Streams.java:46) ~[minecraft_server.18w20a.jar:?] ... 17 more

I should also mention it is not command specific, due to the large amount of command blocks I had, and how none of them loaded the command.