diff --git a/datman/src/commands/prune.rs b/datman/src/commands/prune.rs
index 7280a45..de5a40b 100644
--- a/datman/src/commands/prune.rs
+++ b/datman/src/commands/prune.rs
@@ -132,7 +132,12 @@ pub fn prune_with_retention_policy(
     }
 
     for to_remove in pointers_to_remove {
-        remove_pointer_safely(&pile, &to_remove)?;
+        let res = remove_pointer_safely(&pile, &to_remove).context("removing prunable pointers");
+
+        pile.flush()
+            .context("flushing pile after removing pointers")?;
+
+        res?;
     }
 
     Ok(())
diff --git a/yama/src/operations.rs b/yama/src/operations.rs
index bcea48b..ed3dfbb 100644
--- a/yama/src/operations.rs
+++ b/yama/src/operations.rs
@@ -1,7 +1,7 @@
 use crate::commands::{fully_integrate_pointer_node, retrieve_tree_node, store_tree_node};
 use crate::pile::{Pile, RawPile};
 use crate::tree::{differentiate_node_in_place, integrate_node_in_place};
-use anyhow::anyhow;
+use anyhow::{anyhow, Context};
 use log::info;
 
 pub mod checking;
@@ -15,10 +15,12 @@ pub fn remove_pointer_safely<P: RawPile>(pile: &Pile<P>, name: &str) -> anyhow::
     let mut this_pointer = pile
         .read_pointer(name)?
         .ok_or_else(|| anyhow!("Pointer {:?} does not exist so can not be deleted.", name))?;
-    let mut this_node = retrieve_tree_node(&pile, this_pointer.chunk_ref.clone())?;
+    let mut this_node = retrieve_tree_node(&pile, this_pointer.chunk_ref.clone())
+        .context("retrieving 'this' node")?;
 
     let new_parent_name = this_pointer.parent_pointer.clone();
-    fully_integrate_pointer_node(pile, &mut this_node.node, &mut this_pointer)?;
+    fully_integrate_pointer_node(pile, &mut this_node.node, &mut this_pointer)
+        .context("integrating new parent")?;
 
     let new_parent = if let Some(ref new_parent_name) = new_parent_name {
         let mut new_parent_pointer = pile
@@ -62,6 +64,10 @@ pub fn remove_pointer_safely<P: RawPile>(pile: &Pile<P>, name: &str) -> anyhow::
                     pointer_data.chunk_ref = new_chunk_ref;
                     // write the pointer back.
                     pile.write_pointer(pointer.as_str(), &pointer_data)?;
+
+                    // we must flush chunks before deleting the pointer
+                    pile.flush()
+                        .context("flushing after writing pointer back")?;
                 }
             }
         }