fix: ensure the checkpoint decoder is regularly flushed

[rtyler]

For checkpoint buffers that cannot fit into the batch size the checkpoint will be written with an insufficient number of bytes.

Unfortunately our tests didn't catch this and it only manifested on tables with very large transaction logs

[codecov]

Codecov Report

Attention: Patch coverage is 0% with 60 lines in your changes missing coverage. Please review.

Project coverage is 72.25%. Comparing base (8ba8e08) to head (a08179d).
Report is 4 commits behind head on main.

Files with missing lines	Patch %	Lines
crates/core/src/protocol/checkpoints.rs	0.00%	58 Missing and 2 partials ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2960      +/-   ##
==========================================
- Coverage   72.36%   72.25%   -0.11%     
==========================================
  Files         131      131              
  Lines       40602    40660      +58     
  Branches    40602    40660      +58     
==========================================
- Hits        29380    29378       -2     
- Misses       9335     9393      +58     
- Partials     1887     1889       +2     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.