To fix the issue I used the TeamCity REST API. I created a new build param of type prompt called 'ReleaseType' which can be either Patch, Minor or Major. This is then used in this command line script which is set up as a TeamCity build step:
IF "%ReleaseType%"=="Major" (
set /a newVersion=%VersionMajor%+1
curl -v --request PUT -d 0 --Header "Content-Type: text/plain" http://username:password@servername:8080/httpAuth/app/rest/projects/%system.teamcity.projectName%/parameters/VersionMinor
curl -v --request PUT -d 0 --Header "Content-Type: text/plain" http://username:password@servername:8080/httpAuth/app/rest/projects/%system.teamcity.projectName%/parameters/VersionPatch
)
IF "%ReleaseType%"=="Minor" (
set /a newVersion=%VersionMinor%+1
curl -v --request PUT -d 0 --Header "Content-Type: text/plain" http://username:password@servername:8080/httpAuth/app/rest/projects/%system.teamcity.projectName%/parameters/VersionPatch
)
IF "%ReleaseType%"=="Patch" (
set /a newVersion=%VersionPatch%+1
)
curl -v --request PUT -d %%newVersion%% --Header "Content-Type: text/plain" http://username:password@servername:8080/httpAuth/app/rest/projects/%system.teamcity.projectName%/parameters/Version%ReleaseType%
curl -v --request PUT -d 0 --Header "Content-Type: text/plain" http://username:password@servername:8080/httpAuth/app/rest/buildTypes/id:%dep.Dependant_BuildName.system.teamcity.buildType.id%/settings/buildNumberCounter
This increments the specified build number and resets downstream version parts to 0.
For example, a minor version increase on 3.2.12.122 goes to 3.3.0.0.
Note - in my particular example above the build counter is reset on a dependant build and not the configuration which is running. This may or may not be what you are after. Replace
%dep.Dependant_BuildName.system.teamcity.buildType.id%
with
%system.teamcity.buildType.id%
if you want to reset the current running build configuration.