id,node_id,number,title,user,state,locked,assignee,milestone,comments,created_at,updated_at,closed_at,author_association,active_lock_reason,draft,pull_request,body,reactions,performed_via_github_app,state_reason,repo,type
2117245042,I_kwDOAMm_X85-Mphy,8703,calling to_zarr inside map_blocks function results in missing values,23472459,closed,0,,,8,2024-02-04T18:21:40Z,2024-04-11T06:53:45Z,2024-04-11T06:53:45Z,NONE,,,,"### What happened?

I want to work with a huge dataset stored in hdf5 loaded in chunks. Each chunk contains part of my data that should be saved to a specific region of zarr files. I need to follow the original order of chunks.
I found it a convenient way to use a `map_blocks` function for this purpose. However, I have missing values in the final zarr file. Some chunks or parts of chunks are not stored.


I used a simplified scenario for code documenting this behavior. The initial zarr file of zeros is filled with ones. There are always some parts where there are still zeros.  



### What did you expect to happen?

_No response_

### Minimal Complete Verifiable Example

```Python
import os
import shutil
import xarray as xr
import numpy as np
import dask.array as da

xr.show_versions()

zarr_file = ""file.zarr""
if os.path.exists(zarr_file):
    shutil.rmtree(zarr_file)

chunk_size = 5
shape = (50, 32, 1000)
ones_dataset = xr.Dataset({""data"": xr.ones_like(xr.DataArray(np.empty(shape)))})
ones_dataset = ones_dataset.chunk({'dim_0': chunk_size})
chunk_indices = np.arange(len(ones_dataset.chunks['dim_0']))
chunk_ids = np.repeat(np.arange(ones_dataset.sizes[""dim_0""] // chunk_size), chunk_size)
chunk_ids_dask_array = da.from_array(chunk_ids, chunks=(chunk_size,))
# Append the chunk IDs Dask array as a new variable to the existing dataset
ones_dataset['chunk_id'] = (('dim_0',), chunk_ids_dask_array)


# Create a new dataset filled with zeros
zeros_dataset = xr.Dataset({""data"": xr.zeros_like(xr.DataArray(np.empty(shape)))})
zeros_dataset.to_zarr(zarr_file, compute=False)


def process_chunk(chunk_dataset):
    chunk_id = int(chunk_dataset[""chunk_id""][0])
    chunk_dataset_to_store = chunk_dataset.drop_vars(""chunk_id"")

    start_index = chunk_id * chunk_size
    end_index = chunk_id * chunk_size + chunk_size

    chunk_dataset_to_store.to_zarr(zarr_file, region={'dim_0': slice(start_index, end_index)})
    return chunk_dataset


ones_dataset.map_blocks(process_chunk, template=ones_dataset).compute()

# Load data stored in zarr
zarr_data = xr.open_zarr(zarr_file, chunks={'dim_0': chunk_size})

# Find differences
for var_name in zarr_data.variables:
    try:
        xr.testing.assert_equal(zarr_data[var_name], ones_dataset[var_name])
    except AssertionError:
        print(f""Differences in {var_name}:"")
        print(zarr_data[var_name].values)
        print(ones_dataset[var_name].values)
```


### MVCE confirmation

- [X] Minimal example — the example is as focused as reasonably possible to demonstrate the underlying issue in xarray.
- [X] Complete example — the example is self-contained, including all data and the text of any traceback.
- [X] Verifiable example — the example copy & pastes into an IPython prompt or [Binder notebook](https://mybinder.org/v2/gh/pydata/xarray/main?urlpath=lab/tree/doc/examples/blank_template.ipynb), returning the result.
- [X] New issue — a search of GitHub Issues suggests this is not a duplicate.
- [X] Recent environment — the issue occurs with the latest version of xarray and its dependencies.

### Relevant log output

_No response_

### Anything else we need to know?

_No response_

### Environment

<details>
INSTALLED VERSIONS
------------------
commit: None
python: 3.10.12 (main, Nov 20 2023, 15:14:05) [GCC 11.4.0]
python-bits: 64
OS: Linux
OS-release: 6.5.0-15-generic
machine: x86_64
processor: x86_64
byteorder: little
LC_ALL: None
LANG: en_US.UTF-8
LOCALE: ('en_US', 'UTF-8')
libhdf5: 1.12.2
libnetcdf: 4.9.3-development

xarray: 2024.1.1
pandas: 2.1.4
numpy: 1.26.3
scipy: 1.11.4
netCDF4: 1.6.5
pydap: None
h5netcdf: 1.3.0
h5py: 3.10.0
Nio: None
zarr: 2.16.1
cftime: 1.6.3
nc_time_axis: 1.4.1
iris: None
bottleneck: 1.3.7
dask: 2024.1.1
distributed: 2024.1.0
matplotlib: 3.8.2
cartopy: 0.22.0
seaborn: 0.13.1
numbagg: 0.6.8
fsspec: 2023.12.2
cupy: None
pint: None
sparse: None
flox: 0.8.9
numpy_groupies: 0.10.2
setuptools: 69.0.2
pip: 23.3.1
conda: None
pytest: 7.4.4
mypy: None
IPython: None
sphinx: None


</details>
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2134451073,PR_kwDOAMm_X85m3ZGA,8746,User guide zarr file missing values note,23472459,open,0,,,2,2024-02-14T14:13:50Z,2024-02-18T04:52:28Z,,FIRST_TIME_CONTRIBUTOR,,0,pydata/xarray/pulls/8746,"<!-- Feel free to remove check-list items aren't relevant to your change -->

- [ ] Closes #8703

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